Functional Analysis

Coastal environments are complex and vital ecosystems threatened by human activities such as pollution, eutrophication, and climate change. To understand the state of these habitats, monitoring microbial communities can be helpful. New techniques based on environmental DNA (eDNA) can monitor broader diversity more efficiently, providing a more comprehensive view of the ecosystem. eDNA-based tools are promising alternatives for studying microbial communities, not only for structural profiling, but also to predict functional profiles, i.e., the genes available in the microbial community. Three methodologies were compared for functional profiling of microbial communities from estuarine and coastal sites in the Basque Country: inference from 16S metabarcoding data with Tax4Fun, GeoChip microarrays, and shotgun metagenomics. Results showed high functional diversity and redundancy, independently of the environmental status of the sampling site. Most of the KEGG Orthologs (KOs) predicted coincided in both metagenome and Tax4Fun dataset, with correlated abundances. However, Geochip-derived abundances did not correlate with those of either dataset. Based on metabarcoding and metagenomics, over 24% of KOs showed significantly differential abundance between estuaries grouped by their environmental status. However, only 6% of the KOs from Geochips differed in abundance in the same manner and 26% of these were discordant with the other techniques.