Aquatic environments resilience: Third-generation sequencing of fungi community of urban wastewater treatment plant and Nile River (Egypt)

Fungal communities play a pivotal role in the era of climate change in maintaining the health and balance of aquatic ecosystems through nutrient cycling, organic matter decomposition, and pollutant removal. This study explored the fungal diversity using PacBio third-generation amplicon sequencing across an urban wastewater treatment plant’s inlet and outlet points, as well as an urban location on the Nile River. The sequence analysis of the collected samples revealed a total of 11,908 operational taxonomic units, with significant variations in fungal community composition across the different habitats. The inlet showed the highest diversity (5871 operational taxonomic units) compared with the outlet and surface water habitats (2679–3002 operational taxonomic units). Notably, environmental parameters such as electric conductivity, total dissolved solids, and ammonium nitrogen exhibited the most significant influence on fungal community variations. Redundancy analysis showed a strong association between fungal genera (LKM11 and Aspergillus) and nutrients (nitrate nitrogen and ammonium nitrogen), suggesting their potential as indicators of nutrient pollution. These insights underscore the importance of understanding the structure of fungal community in different aquatic environments, paving the way for optimizing wastewater treatment processes and resilience of the aquatic ecosystems.