Habitat classification scheme
Developing a benthic habitat classification scheme is a fundamental step in benthic habitat mapping, providing a structured framework for organizing and interpreting ecological data. Globally, several schemes have been proposed, including the IUCN Global Ecosystem Typology27, the Coastal and Marine Ecological Classification Standard (CMECS) in the USA28, and the European Nature Information Service (EUNIS)29. These schemes are widely recognized for their hierarchical structure, organizing habitat units into nested levels30. Higher levels typically rely on broad-scale remote sensing or sonar-derived data to reflect abiotic features, while finer levels incorporate localized in-situ data to capture biotic features.
In this study, a two-level benthic habitat classification framework was developed for Bohai Bay, China, integrating both abiotic and biotic features. This framework, illustrated in Fig. 2, enables a comprehensive characterization of nearshore benthic habitats.
Conceptual framework of marine benthic habitat mapping in the Bohai Bay, China.
Abiotic features
The abiotic classification is structured around three key features: tidal influence, light availability, and substrate type.
First, based on tidal and light regimes, three primary zones were delineated. Littoral zone (intertidal) refers to areas alternated between exposure to air and seawater, supporting amphibious organisms that distinguish them from those found in other zones. Infralittoral zone (subtidal photic zone) refers to areas with sufficient light for photosynthesis (≥ 1% surface irradiance)31, supporting photophilic organisms such as seagrass meadows32. Circalittoral zone (subtidal aphotic nearshore zone) refers to areas lying below the photic limit yet remaining influenced by wave energy, supporting nutrient cycling and other ecological processes.
Second, each of the aforementioned zones is further classified based on substrate types. Substrates are grouped into three broad categories: geological, biogenic, and anthropogenic. These categories are further refined based on factors such as grain size, material composition, and structural origin28.
Biotic features
The biotic classification is based on benthic communities and can be categorized into four main categories. Reef biota refer to communities associated with reef-building fauna, sufficiently abundant to construct identifiable biogenic substrates. Benthic faunal communities refer to faunal communities associated with the seabed but not abundant enough to contribute to substrate formation, as in reef biota. Submerged plants refer to rooted vascular plants and sessile macroalgae that typically remain submerged but may be intermittently exposed during low tides. Semi-terrestrial plants refer to plant communities capable of thriving in the coastal intertidal zone while maintaining adaptations to terrestrial conditions.
Abiotic feature mapping
The spatial delineation of abiotic zones (littoral, infralittoral, and circalittoral) was performed using sequential boundaries: the mean high tide line, the mean low tide line, the photic zone boundary, and the 30 m isobath (representing the nearshore extent)32. Mean high tide line was derived from the coastline data of 2020 Third National Land Survey, which combined topographic surveys and field verification. Mean low tide line was approximated by extracting the 0 m isobath from the global bathymetry grid product (https://oceancloud.nmdis.org.cn/) using the multi-beam approach in the study area. Although the 0 m isobath may not perfectly match the mean low tide line, it can be very close in areas with gently sloping shallow terrains, particularly within tidal flats. The photic zone boundary, defined as the depth where 1% of surface light reaches the seabed, was derived from MODIS L3 product (https://oceancolor.gsfc.nasa.gov/l3/) following the approach by Son & Wang33. The 30 m isobath was extracted from the same global bathymetry grid product to delineate the nearshore extent. Given that the maximum depth in Bohai Bay is less than 30 m, the circalittoral zone coincides with the outer boundary of the study area. In this study, all spatial data layers were processed in ArcGIS 10.8.1. We first generated a polygon vector layer of the study area using the mean high tide line and the outer boundary of the Bohai Bay Ecoregion proposed by Huang22. Then this layer was clipped using the mean low tide line and the photic zone boundary line to obtain the extents of the littoral, infralittoral, and circalittoral zones.
Substrate types were categorized into three main groups: geological, biogenic, and anthropogenic. Geological substrates were mapped using global ocean sediment product (https://oceancloud.nmdis.org.cn). This dataset is based on in-situ marine sediment data collected during national marine special investigations from 1997 to 2020. It was produced through steps including data integration, quality control, gridding interpolation, vectorization processing, and manual review corrections. The data are in polygon vector format, with a resolution of 1:100,000. Biogenic and anthropogenic substrate data are also in polygon vector format, deriving from 2019 side-scan sonar survey and the National Sea Area Dynamic Supervision and Management System respectively. To be noted, anthropogenic substrate layer characterized by human modifications that alter ecological attributes, were excluded from biotic analysis. We corrected the boundaries of geological substrates based on the coastline and overlaid the biogenic and anthropogenic substrate polygons to create an integrated substrate type map.
Finally, the abiotic feature map was generated combining the layers of abiotic zones and substrate types. Each polygon was assigned a comprehensive type based on these attributes.
Biotic feature mapping
The biotic features of Bohai Bay were categorized into reef biota (oyster reefs), benthic faunal communities, and semi-terrestrial plants (tidal salt marshes). The distribution data of oyster reefs were derived in polygon vector format using 2019 side-scan sonar survey data. Tidal salt marsh data were also in polygon vector format using the data from 2023 National Coastal Ecosystem Survey, which integrated remote sensing identification with field verification. Benthic faunal communities were classified into four groups: endangered, key protected, economically important, and dominant communities. Endangered, key protected, and economically important communities were identified following the IUCN Red List of Threatened Species (https://www.iucnredlist.org/), China’s National Key Protected Wild Animals List (https://www.forestry.gov.cn/c/www/gkzfwj/272561.jhtml), and National Key Protected Economic Aquatic Plant and Animal Resources List (http://www.moa.gov.cn/govpublic/YYJ/202401/t20240123_6446366.htm). Dominant communities were analyzed using PRIMER version 6, employing steps including fourth-root transformation, similarity matrix creation, group-average linking cluster analysis, Similarity Profiles (SIMPROF), and Similarity Percentages (SIMPER)16,34,35. Recent benthic data (during the summers of 2021 to 2023, 215 stations in total) collected from the National Ecological Early Warning and Monitoring Program were used to reflect current benthic community status. All benthic samples were collected, processed, preserved, counted in accordance with the Specifications for Oceanographic Survey Part 6: Marine Biological Survey36. Marcrobenthic samples were collected using a 0.05m2 grab sampler, while intertidal organisms were sampled using a 25 × 25 cm intertidal quadrat. Samples were then washed through a 0.5 mm mesh sieve and fixed in a 5% formalin solution for subsequent identification and counting. A total of 236 benthic species were identified. No endangered or key protected communities were identified in Bohai Bay. Economically important communities include Ruditapes philippinarum, Acetes chinensis, and Scapharca communities. Dominant communities include Potamocorbula laevis, Moerella rutile, Gattyana pohaiensis, Nopherus ambigua, Mactra chinensis, Amphioplus japonicus, and Lineidae communities.
The habitats of benthic faunal communities were mapped using the niche theory-based method proposed by Tappin37, which posits that each species depends on a specific set of environmental conditions for its long-term survival38. The BIOENV method in PRIMER version 6 was employed to identify the relevant abiotic variables. We selected five variables for analysis, including bottom water temperature, bottom dissolved oxygen, current velocity, geomorphic type, and substrate type10,16,35. Other available variables of water depth, transparency, salinity, and nutrients were excluded due to the relatively low correlation coefficients. Data of these variables were obtained from the National Marine Ecological Early warning and Monitoring (during the summers from 2006 to 2023, 519 stations in total) to represent the mean environmental state. Environmental thresholds were defined as the mean ± standard deviation of samples associated with each community, capturing typical environmental variability. Habitat suitability was modeled as the percentage of abiotic variables meeting the niche requirements of each community37,38. All abiotic variables were first interpolated to generate 0.5 × 0.5 km gridded data. Based on the environmental thresholds for each benthic community, the reclassification tool was used to assign a value of 1 to grid cells falling within the threshold range, and 0 to those outside it. Then, using raster calculation tools, the number of abiotic variables meeting the niche requirements was calculated, and the results were finally normalized to a scale of 0–100% to derive habitat suitability. Potential habitats were identified where suitability exceeded 80%39,40, and observed samples confirmed the presence of the respective communities.
In this study, we integrated the distribution maps of various benthic communities into a single, unified biotic feature map. Although one community cannot occur exclusively in a specific habitat, it always invariably comprises multiple associated species. Here, to highlight the dominant features of each area and align the mapping process with policymaker needs, we established a spatial overlay priority considering the factors of occupancy duration, ecological protection, and resource utilization. First, based on the occupancy time of a habitat, oyster reefs and tidal salt marshes were assigned the highest priority. They both create a habitat for numerous organism communities, and also contribute to form the biogeochemistry environment to different extent. Second, for communities of key protected species, threatened species, economically important species, and dominant species, we overlaid the habitats in an order that prioritizing habitats of protected and threatened species, followed by those of economically important species, to align with the conservation priority policy in China. Finally, we mapped the habitats of dominant species in the remaining areas. In practice, multiple layers were first transformed into polygon vector format and merged into a single layer using a union tool. Then, each resulting polygon was manually assigned a biotic feature based on the established prioritization order.
Comprehensive habitat mapping
The abiotic and biotic maps were merged using the union tool, retaining the attribute information from both layers. Each resulting polygon was manually reviewed to ensure consistency between the abiotic and biotic features. Only biotic features consistent with the corresponding abiotic features were retained, any mismatched biotic information was excluded. A comprehensive benthic habitat type was then assigned to each polygon, resulting in the final integrated habitat map.
