Varbiro, G. | Search bioRxiv

bioRxiv2022

Uncertainties of cell number estimation in cyanobacterial colonies and the potential use of sphere packing

Cyanobacteria are notorious bloom formers causing various water quality concerns, such as toxin production, extreme diurnal variation of oxygen, or pH, etc., therefore, their monitoring is essential to protect the ecological status of aquatic systems. Cyanobacterial cell counts and biovolumes are currently being used in water management and water quality alert systems. In this study, we investigated the accuracy of colonial biovolume and cell count estimation approaches used in the everyday practice. Using real like 3-dimensional images of cyanobacterial colonies, we demonstrated that their shape cannot be approximated by ellipsoids. We also showed that despite the significant relationship between overall colony volume and cell biovolumes because of the considerable scatter of cell count data the regressions give biased estimates for cyanobacterial cell counts. We proposed a novel approach to estimate cell counts in colonies that was based on the random close sphere packing method. This method provided good results only in those cases when overall colony volumes could be accurately measured. The visual investigation of colonies done by skilled experts has given precise but lower estimates for cell counts. Estimation results of several experts were surprisingly good which suggest that this capability can be improved, and estimation bias can be reduced to the level acceptable for water quality estimations. HighlightsCyanobacterial colony - cell biovolume relationships provide biased estimates for cellbiovolumes. Sphere packing approach provides good cellcount estimates if colony volumes are accurately measured. Considering cyanobacterial colonies as ellipsoids gives inaccurate volume estimates. Skilled experts slightly underestimate the cellcounts but dispersion of their estimates is low.

ecology↗

bioRxiv2019

DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work

Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilization of metabarcoding in aquatic biomonitoring.

ecology↗