Shallow-water Benthic Habitats Research Articles

An enhanced large-scale benthic reflectance retrieval model for the remote sensing of submerged ecosystems in optically shallow waters

Shallow water benthic habitats have been significantly degraded and seriously threatened by intensifying climate changes and anthropogenic stressors. Benthic reflectance (Rbλ) of optically shallow waters (OSWs) is a key parameter for remote sensing of benthic habitats’ composition and health status. The remote sensing reflectance (Rrsλ) just above the water surface contains the coupled spectral information of the water column and seabed in OSWs, which makes our effort challenging to separate the signals between seabed and water column properties. Due to too many unknowns of the water column and seabed optical properties, the current approaches are inaccurate or inadequate to retrieve benthic reflectance spectra over a large area from remotely sensed data. In this study, we proposed an enhanced large-scale benthic reflectance (LSBR) retrieval model from satellite data in OSWs with only input of Rrsλ. A new spectral library of benthic reflectance was built upon multi-source reflectance datasets obtained from several open-source field measurements. Then, the specific relationship between Rb443nm and Rb490nm was developed. By combining a semi-analytical benthic reflectance (SABR) model based on radiative transfer simulations and this relationship, water-column chlorophyll concentration (chl) was determined. Moreover, large-scale water depth was estimated by Rrsλ through satellite-derived bathymetry (SDB) technologies. Finally, benthic reflectance was retrieved with the inputs of the satellite-derived Rrsλ, chl, and water depth. In this way, the LSBR model fulfills the Rbλ retrieval with only input of satellite-derived Rrsλ. The new model was successfully applied to Sentinel-2/MSI data in the seagrass region of Xincun Bay and the coral region of Huaguang Reef and further verified by using field measurements and results of the along-track benthic reflectance (ATBR) retrieval model, which combined active lidar and passive high-resolution satellite images. Additionally, to gain insights into the long-term evolution of benthic communities, a typical application of the LSBR model for detecting benthic changes was conducted using eight years of Sentinel-2/MSI data in Heron Reef, depicting a similar consistency between the probable deterioration and restoration region and the sea surface temperature (SST) anomalies. The results demonstrated the robustness and accuracy of the LSBR model in retrieving benthic reflectance at large scales. The LSBR model should be helpful for further investigating benthic changes which can enhance the ability to monitor and assess the health status of submerged ecosystems in OSWs.

Mapping bathymetry and shallow water benthic habitats in inland and coastal waters with Sentinel-2

Accurate determination of the water depth and benthic macroalgae composition in coastal and inland water bodies is important due to the high commercial and ecological value of these regions. Benthic habitat mapping by conventional methods provides good accuracy, but these methods are very expensive and limited by manpower and time factor, which is necessary for mapping large areas. Remote sensing methods significantly complement contact measurements and give additional information about the hard-to-reach areas. The usefulness of free Sentinel-2 data in bathymetry and habitat mapping has been demonstrated in clear oceanic waters. The aim of this study was to further test the suitability of Sentinel-2 imagery in creating maps of dominant benthic types, as well as in estimating bathymetry in optically complex marine and lake waters. Two study sites were selected to cover a representative range of optical variability - Lake Garda in northern Italy (an intermediate between clear ocean and optically very complex waters) and Viimsi peninsula on the Estonian side of the Gulf of Finland, in the Baltic Sea. The results show that Sentinel-2 imagery with 10 m spatial resolution is suitable for bathymetry and habitat mapping in optically complex inland and coastal waters. Our results show that bathymetry mapping is sufficiently accurate in waters less than 4 m deep in the case of the Baltic Sea and up to 7 m deep in Lake Garda. In such depths, the R2 was above 0.93 in all four Sentinel-2 images used in the study. Bottom type mapping accuracy was in all cases over 73%, which is considered to be good, but due to the limited number of sampling points in both test sites, further studies are needed. The Sentinel-2 data quality and no cost of the imagery for users make it very useful for mapping bathymetry and shallow water habitats over large coastal areas or high number of lakes, especially in hard to reach by in situ methods areas. Moreover, the frequent revisit time allows moving from one-off maps to monitoring of temporal changes happening in dynamic shallow inland and coastal waters.

Seagrass restoration monitoring and shallow-water benthic habitat mapping through a photogrammetry-based protocol

Seagrasses rank among the most productive yet highly threatened ecosystems on Earth. Loss of seagrass habitat because of anthropogenic disturbances and evidence of their limited resilience have provided the impetus for investigating and monitoring habitat restoration through transplantation programmes. Although Structure from Motion (SfM) photogrammetry is becoming a more and more relevant technique for mapping underwater environments, no standardised methods currently exist to provide 3-dimensional high spatial resolution and accuracy cartographic products for monitoring seagrass transplantation areas. By synthesizing various remote sensing applications, we provide an underwater SfM-based protocol for monitoring large seagrass restoration areas. The data obtained from consumer-grade red-green-blue (RGB) imagery allowed the fine characterization of the seabed by using 3D dense point clouds and raster layers, including orthophoto mosaics and Digital Surface Models (DSM).The integration of high spatial resolution underwater imagery with object-based image classification (OBIA) technique provided a new tool to count transplanted Posidonia oceanica fragments and estimate the bottom coverage expressed as a percentage of seabed covered by such fragments. Finally, the resulting digital maps were integrated into Geographic Information Systems (GIS) to run topographic change detection analysis and evaluate the mean height of transplanted fragments and detect fine-scale changes in seabed vector ruggedness measure (VRM). Our study provides a guide for creating large-scale, replicable and ready-to-use products for a broad range of applications aimed at standardizing monitoring protocols in future seagrass restoration actions.

Shallow-Water Benthic Habitat Mapping Using Drone with Object Based Image Analyses

Spatial information on benthic habitats in Wangiwangi island waters, Wakatobi District, Indonesia was very limited in recent years. However, this area is one of the marine tourism destinations and one of the Indonesia’s triangle coral reef regions with a very complex coral reef ecosystem. The drone technology that has rapidly developed in this decade, can be used to map benthic habitats in this area. This study aimed to map shallow-water benthic habitats using drone technology in the region of Wangiwangi island waters, Wakatobi District, Indonesia. The field data were collected using a 50 × 50 cm squared transect of 434 observation points in March–April 2017. The DJI Phantom 3 Pro drone with a spatial resolution of 5.2 × 5.2 cm was used to acquire aerial photographs. Image classifications were processed using object-based image analysis (OBIA) method with contextual editing classification at level 1 (reef level) with 200 segmentation scale and several segmentation scales at level 2 (benthic habitat). For level 2 classification, we found that the best algorithm to map benthic habitat was the support vector machine (SVM) algorithm with a segmentation scale of 50. Based on field observations, we produced 12 and 9 benthic habitat classes. Using the OBIA method with a segmentation value of 50 and the SVM algorithm, we obtained the overall accuracy of 77.4% and 81.1% for 12 and 9 object classes, respectively. This result improved overall accuracy up to 17% in mapping benthic habitats using Sentinel-2 satellite data within the similar region, similar classes, and similar method of classification analyses.

Benthic habitat classification using multiscale GEOBIA on orthophoto images of Karimunjawa waters

The scale value is an important part of the segmentation stage which is part of Object-Based Image Analysis (OBIA). Selection of scale value can determine the size of the object which affects the results of classification accuracy. In addition to setting the scale value (multiscale), selection of machine learning algorithm applied to classify shallow water benthic habitat objects can also determine the success of the classification. Combination of setting scale values and classification algorithms are aimed to get optimal results by examining classification accuracies. This study uses orthophoto images processed from Unmanned Aerial Vehicle (UAV) mission intended to capture benthic habitat in Karimunjawa waters. The classification algorithms used are Support Vector Machine (SVM), Bayes, and K-Nearest Neighbors (KNN). The results of the classification of combination are then tested for accuracy based on the sample and Training Test Area (TTA) masks. The result shows that SVM algorithm with scale of 300 produces the best level of accuracy. While the lowest accuracy is achieved by using SVM algorithm with scale of 100. The result shows that the optimal scale settings in segmenting objects sequentially are 300, 200, and 100

Coastal shallow waters explorer imaging spectrometer for aerial remote sensing of shallow waters in UV-VIS-NIR broadband.

Advancements in technology have widened the limits of hyperspectral imaging of remote sensing in mapping shallow water benthic habitats and bathymetry. This paper provides a novel airborne imaging spectrometer for the field. The device, composed of an off-axis two-mirror telescope and an advanced Dyson spectrometer working in the ultraviolet-visible near-infrared region, has been designed, fabricated, and evaluated. It maintained high optical performance, with a pixel spatial resolution better than 0.5 mrad, spectral resolution of 3.5 nm, field of view of 28°, and a high numerical aperture for high SNR in 330-900 nm. The imaging spectrometer will help to obtain a combination of the spectral and textural characteristics of bottom features in shallow waters. These features could result in the ability to map habitats over large coastal systems.

The Use of Multimodal Data to Augment Shallow-Water Benthic Habitat Maps for Pleasant Bay, Cape Cod, Massachusetts: Stratigraphic Data and Seafloor Maps

This paper discusses the utility of using seismic-reflection profiling and sediment cores in addition to bottom grab samples and acoustic data to develop shallow-water benthic habitat maps. Currently, the classification system used herein does not provide for the incorporation of stratigraphic data, but we believe that the utility of these maps would improve if such data were included. We conducted vessel-based seafloor-mapping surveys using a phase-measuring sidescan sonar in very shallow waters (mean depth = 3.2 m) covering an area >6.7 km2 in Pleasant Bay in 2014. We collected a total of 192 bottom grab samples to document macro-invertebrates and sediment characteristics. We conducted seismic-reflection profiling surveys to document stratigraphy and determine optimal locations for multiple sediment cores during the 2014 field season; we collected both Kullenberg and Livingstone cores. The seismic-reflection data, though conducted at the reconnaissance scale, proved useful to place the seafloor acoustic data in context. The acoustic and benthic habitat data and mapping products become more valuable when an understanding of the underlying stratigraphy is used as context for the benthic habitat maps. Sediment coring and analysis can provide insights into past and current basin evolution, which can further aid marine natural resource managers. However, we believe that stratigraphic data should be incorporated into standard benthic habitat mapping protocols. These multi-modal datasets provide a better understanding of these habitats for the multidisciplinary teams that typically produce and use these maps as well as coastal managers.

Remote sensing of shallow waters – A 50 year retrospective and future directions

Technical advancements have widened the limits of remote sensing in mapping shallow water benthic habitats and bathymetry over the last decades. On the other hand, the needs of shallow water remote sensing have pushed instrument development. In this manuscript we provide 50-year retrospective of the developments in the field in terms of both instrumentation and methods. We also show that spectral features characteristic of the main benthic groups in shallow water are consistent from the tropics to sub-arctic regions and from salty to freshwaters. The fundamental limiting factor in both benthic mapping and bathymetry is absorption of light by water molecules. However, spectral absorption by water molecules is the key to bathymetry derivation. Variable backscattering by particles and absorption by dissolved organic matter is a confounding factor for all objectives. The combination of using the spectral and textural characteristics of bottom features and our knowledge about these features have now resulted in the ability to map habitats over large coastal systems. This manuscript has shown that optically shallow water remote sensing has reached levels where the satellite derived bathymetry and habitat maps are accepted by different end users (including the International Maritime Organisation) and are routinely used in ecological studies, monitoring and management of coastal environments.

Benthic habitat classification using high resolution satellite imagery in Sebaru Besar Island, Kepulauan Seribu

Remote sensing technology can provide spatial information for mapping shallow water benthic habitat, a case study conducted on Sebaru Besar Island. The purpose of this study was to analyze mapping accuracy of shallow water benthic habitats usings WorldView 2 and SPOT 6 (201 imageries). The classification of multispectral images is carried out using the Depth Invariant Index (DII) transformation and by applying the Maximum Likelihood (MLH) algorithm to both satellite images. The number of benthic habitat classes produced are eight habitat classes from each image used. The results of the analysis show that the overall accuracy in Worldview 2 and SPOT 6 images is 61.29% and 51.61%. Results of Z-statistic comparison between Worldview-2 and SPOT-6 imagery was 1,04, means that the results did not differ significantly.

Ultrastructure and distribution of kleptoplasts in benthic foraminifera from shallow-water (photic) habitats

Abstract Assimilation, sequestration and maintenance of foreign chloroplasts inside an organism is termed “chloroplast sequestration” or “kleptoplasty”. This phenomenon is known in certain benthic foraminifera, in which such kleptoplasts can be found both intact and functional, but with different retention times depending on foraminiferal species. In the present study, seven species of benthic foraminifera (Haynesina germanica, Elphidium williamsoni, E. selseyense, E. oceanense, E. aff. E. crispum, Planoglabratella opercularis and Ammonia sp.) were collected from shallow-water benthic habitats and examined with the transmission electron microscope (TEM) for cellular ultrastructure to ascertain attributes of kleptoplasts. Results indicate that all these foraminiferal taxa actively obtain kleptoplasts but organized them differently within their endoplasm. In some species, the kleptoplasts were evenly distributed throughout the endoplasm (e.g., H. germanica, E. oceanense, Ammonia sp.), whereas other species consistently had plastids distributed close to the external cell membrane (e.g., Elphidium williamsoni, E. selseyense, P. opercularis). Chloroplast degradation also seemed to differ between species, as many degraded plastids were found in Ammonia sp. and E. oceanense compared to other investigated species. Digestion ability, along with different feeding and sequestration strategies may explain the differences in retention time between taxa. Additionally, the organization of the sequestered plastids within the endoplasm may also suggest behavioral strategies to expose and/or protect the sequestered plastids to/from light and/or to favor gas and/or nutrient exchange with their surrounding habitats.

Integrating Remote Sensing and Field Survey to Map Shallow Water Benthic Habitat for the Kingdom of Bahrain

Integrating Remote Sensing and Field Survey to Map Shallow Water Benthic Habitat for the Kingdom of Bahrain

A comparison of epiphytic diatom communities on Plocamium cartilagineum (Plocamiales, Florideophyceae) from two Antarctic areas

Our understanding of diatoms, one of the most important Antarctic primary producers, is based mostly on investigations of plankton, sea-ice, and sediment samples. Herein, we contribute to the limited research devoted to benthic Antarctic diatoms by presenting a study on epiphytic diatom communities sampled in two remote Antarctic regions: Admiralty Bay (maritime Antarctica, Antarctic Peninsula) and Terra Nova Bay (Ross Sea). Recent studies have demonstrated that the most critical factor for the local epiphytic diatom communities was the nature of the substrate. In order to eliminate this factor so we could evaluate other potential controls, we sampled epiphytic diatoms from only one substrate that is common to both regions: the macroalgae Plocamium cartilagineum (L.) Dixon. Thalli of P. cartilagineum and their associated microalgal community was collected in January 2011 (Admiralty Bay) and 2012 (Terra Nova Bay) from a water depth of 5–25 m. Dehydrated macroalgal pieces were placed on stubs and sputter-coated, which allowed observation of diatoms attached to the substrate in their original position using scanning electron microscopy. A total of 72 taxa were observed, of which 31 taxa were common to both regions. Cell abundance and diatom growth form dominance were significantly different in Admiralty Bay and Terra Nova Bay samples. Total diatom abundance was higher in Admiralty Bay samples, dominated by adnate diatoms (Cocconeis spp.), but the number of taxa found as well as the values of ecological indices were higher for samples from the Ross Sea, where motile forms were dominant (Navicula spp.). Our results suggest that Antarctic shallow-water benthic habitats may present a high degree of microniche heterogeneity and highlight the need of fine-scale analyses in microbial studies. We also suggest grazers as a factor that contributes greatly to the observed differences.

Reef Fishes of Saba Bank, Netherlands Antilles: Assemblage Structure across a Gradient of Habitat Types

Saba Bank is a 2,200 km2 submerged carbonate platform in the northeastern Caribbean Sea off Saba Island, Netherlands Antilles. The presence of reef-like geomorphic features and significant shelf edge coral development on Saba Bank have led to the conclusion that it is an actively growing, though wholly submerged, coral reef atoll. However, little information exists on the composition of benthic communities or associated reef fish assemblages of Saba Bank. We selected a 40 km2 area of the bank for an exploratory study. Habitat and reef fish assemblages were investigated in five shallow-water benthic habitat types that form a gradient from Saba Bank shelf edge to lagoon. Significant coral cover was restricted to fore reef habitat (average cover 11.5%) and outer reef flat habitat (2.4%) and declined to near zero in habitats of the central lagoon zone. Macroalgae dominated benthic cover in all habitats (average cover: 32.5 – 48.1%) but dominant algal genera differed among habitats. A total of 97 fish species were recorded. The composition of Saba Bank fish assemblages differed among habitat types. Highest fish density and diversity occurred in the outer reef flat, fore reef and inner reef flat habitats. Biomass estimates for commercially valued species in the reef zone (fore reef and reef flat habitats) ranged between 52 and 83 g/m2. The composition of Saba Bank fish assemblages reflects the absence of important nursery habitats, as well as the effects of past fishing. The relatively high abundance of large predatory fish (i.e. groupers and sharks), which is generally considered an indicator of good ecosystem health for tropical reef systems, shows that an intact trophic network is still present on Saba Bank.

The influence of geomorphology and sedimentary processes on shallow-water benthic habitat distribution: Esperance Bay, Western Australia

The mapping of seabed environments is fundamental to successful fisheries management and environmental monitoring, however, there is an emerging need to better characterise habitats based upon appropriate physical parameters. In this study, relationships between seabed geomorphology and the distribution of benthic habitats were examined using multibeam sonar, underwater video, predicted wave energy, and sediment data for Esperance Bay, part of the Recherche Archipelago. This shallow (<50 m), high energy, biogenic sediment dominated environment is located in temperate southwestern Australia. Exposure to wave energy appears to determine the distribution of unconsolidated substrate, and is the most useful regional scale predictor of rhodolith and seagrass habitats. Although they are intermittently smothered by mobile sediments, limestone reefs provide habitat for a wide range of sessile organisms, even in very high wave exposure environments. The distribution of rhodolith beds is related to poorly sorted sediments that contain high gravel, mud, and CaCO 3 percentages. Our results reveal that in the Recherche Archipelago, wave abrasion coupled with localised sediment transport and accumulation play a major role in increasing the diversity of inner shelf benthic habitats. This highlights the value of assessing geomorphic processes in order to better understand the distribution and structure of benthic habitats.

Sipunculans from the coast of northern Cyprus (eastern Mediterranean Sea)

The present study deals with the species of Sipuncula collected from northern Cyprus in 1997 and 1998 by RV K. Piri Reis at depths ranging from 0 to 600 m. Faunistic analysis of the material yielded a total of 6 species and 5 subspecies belonging to four families Golfingiidae, Phascolionidae, Phascolosomatidae, and Aspidosiphonidae, of which four species (Nephasoma (Nephasoma) constrictum, Phascolosoma (Phascolosoma) scolops, P. (P.) agassizii agassizii and P. (P.) stephensoni) are reported for the first time from the eastern Mediterranean. Among the habitats sampled, Posidonia oceanica and mud were represented by the highest number of species (6 species), followed by rocks (5 species) and Cystoseira crinita (5 species). Quantitative analysis of shallow-water benthic habitats indicated that sipunculan density in the area ranged from 25 individuals m-2 to 350 individuals m-2. According to the MDS analysis, there are two major species assemblages in the area, mainly structured by the types of habitats and depth.

Synoptic water clarity assessment in the Florida Keys using diffuse attenuation coefficient estimated from Landsat imagery

The diffuse attenuation coefficient, K (m− 1), is a measure of the effective attenuation of light in the water column. It characterizes water clarity and is used as a proxy for water quality. Mapping of shallow water benthic habitats using optical means, including daytime visible satellite imagery, requires knowledge of K to correct for water column effects such as light absorption and scattering. Traditionally, K is derived from imagery using a priori knowledge of bottom types at different depths and specific locations, and assuming that light attenuates exponentially with depth. This technique is applied to three Landsat 7 satellite images (February, May, and July 2000) from the Florida Keys Reef Tract between Key Largo and Key West. Interpolated depth data, initially from NOAA vector chart data, with uncertainties of ±0.5 m, were draped over 30 m spatial resolution Landsat satellite imagery. K was derived for 27 sites where bright sand could be observed at depths between 3 and 20 m. The blue and green bands (Landsat bands 1 and 2 at 450–520 nm and 520–600 nm, respectively) provided K values consistent with time and location. Average K values for bands 1 and 2, respectively, were 0.029 and 0.043 m− 1 (Lower Keys), 0.050 and 0.072 m− 1 (Middle Keys), and 0.063 and 0.082 m− 1 (Upper Keys). The red band (band 3, 630–690 nm) provided more ambiguous and erroneous results with several negative K values, attributed primarily to three factors use of a simple atmospheric correction, the high absorption and rapid attenuation of red light in water, and low radiometric sensitivity of the Landsat ETM + sensor. Despite the fact that these observations were a snapshot in time, trends were observed for the Upper, Middle, and Lower Keys, possibly due to the influence of more turbid Florida Bay waters.

Ecological features of Syllidae (Polychaeta) from shallow-water benthic environments of the Aegean Sea, eastern Mediterranean

Ecological features of Syllidae inhabiting shallow-water benthic habitats of the Aegean Sea were analysed by utilizing some univariate and multivariate statistical methods. A total of 121 benthic materials collected in a variety of substrata and depths (0–76 m) contained 90 syllid species belonging to the four subfamilies Autolytinae, Exogoninae, Eusyllinae and Syllinae. Among the subfamilies, Syllinae were characterized by a high number of species and Exogoninae by a high number of individuals. Although dominant species varied according to substrata, the two species, Grubeosyllis clavata and Syllis prolifera, accounted for up to 51% of the total syllid populations in the area. Among the biotopes sampled, Posidonia oceanica seems to be particularly suitable for the settlement of syllid species, whereas bare sand and mud harbour only a few species, mainly Exogoninae. The cluster- and ordination analyses detected species associations on soft and hard substrata, and suggested that syllid assemblages are strongly affected by the habitat structure. Species compositions associated with algae appear to be related to complexity of the algae, so that the ones with relatively small thalli, such as Padina pavonica and Halopteris spp., constituted a group with a high similarity-index value. Samples of Posidonia oceanica collected at different stations showed a high consistency in terms of syllid assemblages.

Lipid content and composition of some midwater crustaceans from the Southern Ocean

The decapods Pasiphaea scotiae (Stebbing), P. rathbunae (Stebbing), Petalidium foliaceum Bate and Acanthephyra pelagica (Risso) and the mysid Gnathophausia gigas (W.-Suhm) have been sampled from the Southern Ocean. Lipid contents were generally very high, 5 to 25% fresh weight in immature and male Pasiphaea scotiae, 7 to 17% in Acanthephyra pelagica and up to 20% in both Gnathophausia gigas and Petalidium foliaceum. Carotenoid pigment contents were also high compared with benthic decapods. In most species the major storage lipid was wax ester, although in Pasiphaea scotiae triacylglycerol was of equal or greater importance. Fatty acid compositions were typical of marine invertebrates from pelagic and shallow-water benthic habitats, although P. scotiae and Acanthephyra pelagica contained substantial levels of 20:1 in the triacylglycerol. Wax ester alcohol compositions were unusual in that both 20:1 and 22:1 were present as a suite of positional isomers. The variation in lipid content and composition with sex and season in both Pasiphaea scotiae and Acanthephyra pelagica indicated that the major factor influencing lipid storage in these organisms was the pattern of food availability, although they would clearly also benefit from the associated increased buoyancy. High-latitude midwater crustaceans contain much more lipid than the same or related species from lower latitudes. This parallels the increasing seasonally of production towards the poles, indicating that this seasonality influences the biology of the underlying mesopelagic community.