Cross-taxa assessment of species diversity and phylogenetic structure of benthic communities in a dam-impacted river undergoing habitat restoration

Exploring diversity and community composition patterns across evolutionary and functionally diverse organisms is critical for understanding the general processes that shape biodiversity in response to environmental changes. Knowledge of multi-trophic relationships offers valuable insights to support the effective assessment and management of freshwater ecosystems. In this study, we conducted a cross-taxa assessment of benthic macroinvertebrates and microorganisms using metabarcoding-based surveys to evaluate habitat restoration in a dam-impacted river. We found no correlation between the α-diversity of the benthic macroinvertebrate and microbial communities. This suggests that factors influencing the α-diversity of different trophic groups might operate independently or through different mechanisms, even within the same habitat. In contrast, we observed positively correlated β-diversity patterns between the two benthic communities influenced by dam fragmentation and gravel bar restoration. This suggests that environmental heterogeneity between sites may have a common influence on the patterns of pairwise dissimilarities in the benthic communities, even though they have significant differences in key traits, e.g., species composition, functional roles, or trophic level. Additionally, phylogenetic structure analysis revealed a greater dam impact on benthic macroinvertebrates than microbial communities. Benthic microorganisms consistently formed phylogenetically clustered communities regardless of dam impact, while the macroinvertebrates shifted from competitive exclusion to environmental filtering in response to dam fragmentation. Our cross-taxa assessment further explained the relationships among benthic communities and their associations with environmental factors in a river ecosystem undergoing habitat restoration. Our study highlights the significant implications of evaluating different biological communities across trophic levels for river restoration strategies and ecosystem assessment.