Beyond cichlid diversification: environmental drivers of biodiversity across the Nicaraguan lake system

The Nicaraguan lake system, comprising two Great Lakes and several isolated crater lakes, is a natural laboratory for investigating how environmental heterogeneity and isolation shape biodiversity and a classic model for Midas cichlid diversification. We asked whether lake characteristics associated with cichlid diversification are also linked to prokaryotic and eukaryotic diversity patterns. Using environmental DNA metabarcoding of water and sediments, we characterized communities in the large, shallow Great Lakes and smaller, deeper crater lakes. Lakes differed markedly in environmental conditions, and community composition differed between water and sediments, while patterns suggested higher prokaryotic diversity in sediments and greater eukaryotic diversity in the water column; however, sediment samples were not replicated. At sampled sites, the Great Lakes harbored highly diverse communities, potentially reflecting their size and hydrological connectivity, whereas crater-lake communities showed stronger differentiation. Mean lake depth was strongly associated with community composition, particularly in eukaryotes. Thus, a lake characteristic previously implicated in Midas cichlid diversification is also associated with broader biological community structure. Overall, our results provide partial support for shared environmental structuring, but relationships differed among taxonomic groups and did not necessarily parallel patterns of cichlid diversification. These findings highlight both common and taxon-specific responses to lake environmental variation.