Biodiversity and distribution of zoobenthos in the ecological water replenishment area of the Yellow River estuary coastal wetland revealed by eDNA metabarcoding

which increased the complexity of data analysis and potentially obscuring the true diversity of benthic animals. Additionally, the large number of "unclassified" sequences further highlights the inadequacy of current reference databases. To improve species identification accuracy, especially in specific ecosystems like the Yellow River Estuary, it is important to establish a localized eDNA database. This is particularly necessary as regional biodiversity may not be fully represented in global databases. This process should also be complemented by compre- hensive benthic taxonomic inventories based on traditional methods, allowing for effective comparison and analysis of sequence data [45]. The raw sequencing data have already been uploaded to the NCBI database and can be accessed with the accession number PRJNA1134659. 4.2. Influence of habitat conditions on zoobenthic communities in the Yellow River Estuary The Yellow River Estuary Coastal Wetland has undergone significant degradation due to agri- cultural reclamation, industrial pollution, and infrastructure development, which have adversely affected its ecological functions. However, decades of ecological restoration, includ- ing vegetation restoration, water resources management, pollution control, and micro-terrain shaping, contributed to the recovery of the wetland ecosystem, fostering rich species diversity [46]. Coastal wetlands feature waters with varying salinity levels, including freshwater, brackish water, and seawater. Salinity plays a crucial role in shaping these ecosystems. Brackish water

with median salinity conditions exhibits the lowest species richness (Fig 3). This is due to fluc- tuating salinity levels, which create challenging conditions for many species [47]. As transi- tional zones, brackish waters limit the species that can adapt to both freshwater and marine conditions [48]. In addition to salinity, factors such as nutrient availability, sediment composi- tion, and hydrodynamic conditions, along with human activities like habitat alteration and associated environmental pressures, significantly affect species diversity and community struc- ture [49,50], often favoring more resilient species over those that are more sensitive [51]. Nev- ertheless, many marine species use brackish waters as nurseries for their juvenile stages [52]. These areas serve as crucial migratory pathways, contributing to dynamic but intermediate lev- els of species richness. Zoobenthic communities are highly sensitive to environmental stress- ors, such as pollution and habitat alterations, which can cause significant shifts in species composition. Studies from the Ganga River and the Damodar and Subarnarekha Rivers have shown that macrozoobenthic communities respond to various stressors, including pollution and habitat changes, by shifting towards species that are more tolerant of these conditions [53,54]. For instance, pollution-tolerant species like Limnodrilus tend to increase in abundance in areas impacted by industrial discharge, where they can outcompete more sensitive species.

In contrast, species that are more sensitive to environmental changes, such as those with spe- cific habitat requirements, may decline in these impacted areas [55]. This pattern of commu- nity restructuring highlights the resilience of certain zoobenthic taxa in the face of anthropogenic stressors. Additionally, indicator species are essential for evaluating wetland restoration. For instance, Chaetonotidae thrive in nutrient- and oxygen-rich environments, correlating with TOC and DO levels, while Monhysteridae, Dolichomacrostomidae, and Des- modoridae adapt to low-organic, low-oxygen conditions [56–60]. Their presence or absence reflects the region’s ecological health and highlights zoobenthic community dynamics in response to environmental changes. Furthermore, salinity has a significant impact on zoo- benthic diversity. Species such as Naididae and Polycystididae exhibit positive correlations with salinity, inhabiting diverse environments from freshwater to marine conditions [61–64]. PLOS ONE Biodiversity and zoobenthos distribution in yellow river estuary wetlands revealed by eDNA metabarcoding PLOS ONE | https://doi.org/10.1371/journal.pone.0315346 December 18, 2024 13 / 19