Complete biome capture as an alternative method for stream water quality studies
The metabarcoding approach applied in the present study is a potential cost effective and fast alternative to existing metagenomics-based analyses for biomonitoring as it targets specific genes selected to represent a given taxonomic affiliation, thereby capturing all three domains of life. The use of domain specific indicator genes facilitates detailed analysis covering the majority of ecosystem diversity, thereby exploiting the opportunity to capture previously undescribed taxonomic diversity. While the databases for ribosomal target gene sequences fromBacteria and Archaea are good, they remain relatively poor for eukaryotic organisms, especially within the invertebrates. Attempts to fill the gaps in reference databases are ongoing as part of national and international Barcode of Life projects (e.g. NorBOL, GBOL, and SwissBOL) (Jinbo, Kato, & Ito, 2011). However, biome profiling for fauna or flora indexing does not necessarily have to provide full taxonomic descriptions and affiliations. The results obtained in this study clearly show that members of all three domains reflect the ecological status of the sampled location. Furthermore, the results provide evidence for the presence of potential indicator organisms within all three domains of life, which may provide a potential for alternative water quality assessment.
In conclusion, simultaneous analysis of Bacteria , Archaeaand Eukaryota using high-throughput amplicon sequencing was shown to be a promising method for convenient and fast assessment of stream water quality. Domain-specific biome profiles separated the samples from 50 water bodies with different geological and physiochemical environments into their respective pre-determined ecological status classes. The obtained data showed that it was possible to extract potential new indicator organisms from all three domains. The strongest correlation between ecological status and community composition was observed for the Bacteria .