DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region.

The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.

Seasonal acclimation in the epiphytic lichen Parmelia sulcata is influenced by change in photobiont population density.

CO2 gas exchange, radial growth, chlorophyll (Chl) content and photobiont density of an epiphytic population of Parmelia sulcata were monitored every 2 months during 1 year in a temperate deciduous forest of Central Italy, to verify possible seasonal variations. Light response curves of south-exposed thalli, built up in the laboratory at 6 and 27°C at optimal thallus hydration, showed that CO2 gas exchange changed significantly during the year, with a maximum for gross photosynthesis in December at both temperatures. Photoinhibition phenomena occurred in early spring, immediately before tree leaves sprouted. The principal component analysis of CO2 gas exchange parameters clearly separated the months with from the months without tree canopy cover. Radial growth, measured on marginal lobes of north- and south-exposed thalli, was the highest in December, and the lowest in April. Photobiont density, measured in lobes of south- and north-exposed thalli with a sedimentation chamber, also changed during the year: the number of photobionts was highest in June and December, and lowest in April, although no significant change in cell size and Chl content per cell was evident throughout the year. South-exposed thalli had slightly, but constantly higher photobiont density both on a weight and an area basis. The acclimation of lichen photosynthesis and Chl content to seasonal temperature and light changes should partially be re-visited on the basis of the significant variation in photobiont population density. This phenomenon still awaits, however, a satisfactory explanation, although it is probably related to the seasonal change in nutrient availability.

Results from the first ballast water sampling study in the Mediterranean Sea - the Port of Koper study.

The ongoing transfer of harmful organisms by shipping, especially via ballast water transport, may result in a change of biodiversity, alteration of ecosystems, negative impacts on human health and economic loss. Species introductions which cause irreversible consequences to receiving environments and economies call for particular attention. One critical issue is a need to evaluate the quantities and processes of species introductions. Consequently ballast water was sampled on 15 ships calling at the Port of Koper, Slovenia. This was the first ballast water sampling study in the Mediterranean Sea. This paper summarises the sampling results. Samples were analysed for all types of aquatic organisms including bacteria. The results may be considered as background information for an initial risk assessment of future species introductions - an important tool for the implementation of ballast water management measures.