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.

effect of short-term meteorological disturbances on the submerged aquatic vegetation and associated fauna in the Patos Lagoon estuary, southern Brazil

Occluded fronts are naturally cyclogenic areas that have been intensified by global warming. Studies evaluating the effects of occluded fronts in the submerged aquatic vegetation (SAV) and its associated fauna in shallow estuarine areas may provide insights on the impacts of climate change-induced extreme weather events on coastal ecosystems functioning. The present dataset describes data on benthic fauna and flora in the Patos Lagoon Estuary (PLE), in southern Brazil, seasonally obtained during intense occluded fronts. Using a hierarchical sample design, based on Beyond BACI protocols (Before/After and Control/Impact), fauna and flora were sampled before and after four occluded fronts passage throughout 2019.Three habitats were sampled: SAV Meadow, SAV Edge and adjacent Sandflat. A total of 432 macrozoobenthic samples (216 samples for stratum); 216 samples for bellow and aboveground biomass, vegetation coverage, canopy height and marine macrophytes morphology; 144 samples by sedimentology and organic matter; 72 water column depth measurements; and 8 temperature and salinity measurements were collected during the study period. The data is available at the Global Biodiversity Information Facility (GBIF), in Darwin Core standard format (DwC), organized according to the OBIS-ENV-DATA model, with CC-BY-NC-4-0 license for use. The present dataset adds to the comprehension of the temporal variability of estuarine benthic communities in subtropical systems, and how short-term meteorological process can affect zoo and fitobenthic communities in the context of climate changes.

Multi-Scale Spectral Separability of Submerged Aquatic Vegetation Species in a Freshwater Ecosystem

Optical remote sensing has been suggested as a preferred method for monitoring submerged aquatic vegetation (SAV), a critical component of freshwater ecosystems that is facing increasing pressures due to climate change and human disturbance. However, due to the limited prior application of remote sensing to mapping freshwater vegetation, major foundational knowledge gaps remain, specifically in terms of the specificity of the targets and the scales at which they can be monitored. The spectral separability of SAV from the St. Lawrence River, Ontario, Canada, was therefore examined at the leaf level (i.e., spectroradiometer) as well as at coarser spectral resolutions simulating airborne and satellite sensors commonly used in the SAV mapping literature. On a Leave-one-out Nearest Neighbor criterion (LNN) scale of values from 0 (inseparable) to 1 (entirely separable), an LNN criterion value between 0.82 (separating amongst all species) and 1 (separating between vegetation and non-vegetation) was achieved for samples collected in the peak-growing season from the leaf level spectroradiometer data. In contrast, samples from the late-growing season and those resampled to coarser spectral resolutions were less separable (e.g., inter-specific LNN reduction of 0.25 in late-growing season samples as compared to the peak-growing season, and of 0.28 after resampling to the spectral response of Landsat TM5). The same SAV species were also mapped from actual airborne hyperspectral imagery using target detection analyses to illustrate how theoretical fine-scale separability translates to an in situ, moderate-spatial scale application. Novel radiometric correction, georeferencing, and water column compensation methods were applied to optimize the imagery analyzed. The SAV was generally well detected (overall recall of 88% and 94% detecting individual vegetation classes and vegetation/non-vegetation, respectively). In comparison, underwater photographs manually interpreted by a group of experts (i.e., a conventional SAV survey method) tended to be more effective than target detection at identifying individual classes, though responses varied substantially. These findings demonstrated that hyperspectral remote sensing is a viable alternative to conventional methods for identifying SAV at the leaf level and for monitoring at larger spatial scales of interest to ecosystem managers and aquatic researchers.

Environmental factors affecting coastal and estuarine submerged aquatic vegetation (SAV)

Submerged aquatic vegetation (SAV) growing in estuarine and coastal marine systems provides crucial ecosystem functions ranging from sediment stabilization to habitat and food for specific species. SAV systems, however, are sensitive to a number of environmental factors, both anthropogenic and natural. The most common limiting factors are light limitation, water quality, and salinity, as reported widely across the literature. These factors are controlled by a number of complex processes, however, varying greatly between systems and SAV populations. This report seeks to conduct an exhaustive examination of factors influencing estuarine and coastal marine SAV habitats and find the common threads that tie these ecosystems together. Studies relating SAV habitats in the United States to a variety of factors are reviewed here, including geomorphological and bathymetric characteristics, sediment dynamics, sedimentological characteristics, and water quality, as well as hydrologic regime and weather. Tools and methods used to assess each of these important factors are also reviewed. A better understanding of fundamental environmental factors that control SAV growth will provide crucial information for coastal restoration and engineering project planning in areas populated by SAVs.

Fine-scale distribution and occupancy modelling of the threatened pugnose shiner (Notropis anogenus) in the St. Lawrence River, Ontario, Canada1

Understanding population-level habitat requirements is important for the effective conservation of imperilled species, especially for those with fragmented distributions. This study examined fine-scale distribution of the threatened pugnose shiner (Notropis anogenus) in the upper St. Lawrence River, Ontario, Canada. Occupancy modelling, multivariate analyses, and co-occurrence modelling were used to identify environmental correlates of pugnose shiner distribution and species associations in an embayment area, Thompson’s Bay. The pugnose shiner was most abundant in outer bay sites that were cooler, less turbid, had a higher pH, and had more submerged aquatic vegetation than the inner bay sites. The probability of pugnose shiner occupancy increased with distance from the inner bay and with the presence of Chara vulgaris, and decreased with increasing conductivity. The pugnose shiner positively co-occurred with seven species, including the blackchin shiner and blacknose shiner, and negatively co-occurred with bluegill. Centrarchid species were dominant across Thompson’s Bay. This has important conservation implications because some native centrarchid predators are increasing in abundance, coincident with climate change, which may threaten the persistence of rare and imperilled cyprinids such as pugnose shiner.