Estimating quality of archive urban stream macroinvertebrate samples for genomic, transcriptomic and proteomic assessment

Abstract

The existence of archival collections of macroinvertebrates opens the possibility of using these organisms as biological indicators and model organisms for developing indices of aquatic ecosystem health and stress, which provide a powerful basis for sustainable environmental monitoring and management of water resources. The environmental assessment of urbanization influence on urban stream biota over time can include molecular (proteomic, transcriptomic and genomic) analyses of aquatic insects isolated from archive samples. These analyses could include confirmation of detected species by barcoding, determination of the changes in the expression of specific genes and detection of changes in signaling pathways in cells of the studied organisms. Since the preservation of the organisms’ macromolecules (DNA, RNA and proteins) is a prerequisite for the implementation of molecular methods, the aim of this study was to assess the quality of macromolecule preservation within archival samples of aquatic macroinvertebrates collected in urban streams during last 28 years. Results indicated that the optimal way for archive storage is 3.6% formaldehyde solution if they have a purpose of morphological assessment or protein analyses, and in absolute ethanol for nucleic acids evaluation. Furthermore, it is of great importance that samples are treated with fixative in situ and processed in a laboratory as soon as possible.

Keywords

• Fixative
• Monitoring
• Urbanization
• DNA and RNA isolation
• Protein detection