Towards routine DNA metabarcoding of macroinvertebrates using bulk samples for freshwater bioassessment: Effects of debris and storage conditions on the recovery of target taxa

1. Macroinvertebrates are commonly sampled for bioassessment of freshwater ecosystems. However, current bioassessment protocols involve laborious sorting of the animals from the debris (sample matrix) and morphological identification, where species level identifications are often difficult. DNA metabarcoding has the potential to improve bioassessment by reducing the time taken to process samples and improve the accuracy and speed of macroinvertebrate species identification.
2. In this study, we evaluated DNA metabarcoding of macroinvertebrate samples, which include macroinvertebrates and the debris collected in the sample nets, to test if bulk, unsorted samples can be used to assess macroinvertebrate diversity. First, we tested if the sample matrix prevented the detection of six target macroinvertebrate taxa when DNA metabarcoding. Second, we tested if sample storage influenced the detection of the same six target macroinvertebrates. We also explored different levels of replication at the sample, sub-sample, and polymerase chain reaction levels and compared the overall macroinvertebrate families detected using DNA metabarcoding to those identified morphologically.
3. We found that the presence of the sample matrix did not interfere with or inhibit the detection of the six target macroinvertebrate taxa. Furthermore, we found that the various sample storage methods did not affect target macroinvertebrate detection. The reliability of detection of the target macroinvertebrates improved as hierarchical levels of replication were combined. We found strong overlap between the detection of overall macroinvertebrate family diversity when comparing DNA metabarcoding to morphological identification.
4. Extracting DNA from the bulk macroinvertebrate samples that included the sample matrix and using this for DNA metabarcoding could improve bioassessment by removing the need for laborious sorting of samples. Furthermore, DNA metabarcoding detection of the six target taxa was not dependent on sample storage of up to 1 year in 95% ethanol, at room temperature or after heating. DNA metabarcoding had the advantage of identifying macroinvertebrate species, but good DNA barcode libraries are needed for widespread species identifications. Further investigation should focus on including multiple samples with different macroinvertebrate composition and densities to refine and standardise bulk sample processing protocols, and on building comprehensive DNA barcode libraries for aquatic macroinvertebrates.

     

Ab initio simulations of Cu binding sites on the N-terminal region of prion protein

The human prion protein binds Cu²⁺ ions in the octarepeat domain of the N-terminal tail up to full occupancy at pH 7.4. Recent experiments have shown that the HGGG octarepeat subdomain is responsible for holding the metal bound in a square-planar configuration. By using first principle ab initio molecular dynamics simulations of the Car–Parrinello type, the coordination of copper to the binding sites of the prion protein octarepeat region is investigated. Simulations are carried out for a number of structured binding sites. Results for the complexes Cu(HGGGW)(wat), Cu(HGGG), and [Cu(HGGG)]₂ are presented. While the presence of a Trp residue and a water molecule does not seem to affect the nature of the copper coordination, high stability of the bond between copper and the amide nitrogen of deprotonated Gly residues is confirmed in all cases. For the more interesting [Cu(HGGG)]₂ complex, a dynamically entangled arrangement of the two domains with exchange of amide nitrogen bonds between the two copper centers emerges, which is consistent with the short Cu–Cu distance observed in experiments at full copper occupancy.     

Effect of soil K, Ca and Mg saturation and endomycorrhization on growth and nutrient uptake of sugar maple seedlings

Nutrient imbalances of declining sugar maple (Acer saccharum Marsh.) stands in southeastern Quebec have been associated with high exchangeable Mg levels in soils relative to soil K and Ca. A greenhouse experiment was set up to test the hypothesis that the equilibrium between soil exchangeable K, Ca, and Mg ions influences the growth and nutrient status of sugar maple seedlings. Also tested was whether endomycorrhization can alter nutrient acquisition under various soil exchangeable basic cations ratios. Treatments consisted of seven ratios of soil exchangeable K, Ca, and Mg making up a total base saturation of 58%, and a soil inoculation treatment with the endomycorrhizal fungus Glomus versiforme (control and inoculated), in a complete factorial design. Sugar maple seedlings were grown for 3 months in the treated soils. Plant shoot elongation rate, dry biomass and nutrient concentrations in foliage were influenced by the various ratios of soil cations. The predicted plant biomass and foliar K concentration were highest at a soil Ca saturation of 38%, a soil K saturation of 12%, and a soil Mg saturation of 8%. Potassium concentration in foliage was dependent on the level of Ca and Mg saturation in the soil when soil K saturation was close to 12%. Foliar Ca and Mg levels were more dependent on their corresponding levels in soil than foliar K. Colonization by G. versiforme did not influence seedling growth and macronutrient uptake. The results confirm that growth and nutrition of sugar maple are negatively affected by imbalances in exchangeable basic cations in soils.