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Phytoplankton is a key element for the assessment of ecological and environmental status of aquatic ecosystems, also in the frame of the MSFD. The methods used to analyse phytoplankton communities are mainly based on time consuming cell counts, dictating a trade-off between the number of cells counted and the number of phytoplankton samples in a monitoring plan, whenever the financial budget, the available personnel or the response time are limited. We investigated the optimal sample size effort, intended as number of phytoplankton cells enumerated per sampling station, of many commonly used metrics. To this aim, precision and uncertainty of the metrics as a function of the sample size have been addressed using a case study carried out in the Lesina lagoon (Apulia, Italy), where 12000 cells per sample have been enumerated within five sampling stations. Overall, we show that some of the commonly used indices/metrics for the description of phytoplankton communities are strongly dependent upon the sampling effort (as number of enumerated individuals per sample), while other metrics are relatively independent. Metrics based on the number of taxa only (e.g. Taxonomic richness), on the ratio between number of taxa and number of individuals (e.g. Margalef's diversity index) or on the species evenness (e.g. Pielou's evenness index) strongly depend on the sample size and their uncertainty (in term of sampling variance) is usually large. On the other hand, metrics of taxonomic diversity accounting for the proportional abundance of each taxa (e.g. Shannon-Wiener's diversity index), metrics accounting for the dominance of the most abundant taxa (e.g. Berger-Parker's dominance index) and metrics derived from the individual size distribution (e.g. Index of Size spectra Sensitivity, ISS Phyto) are able to achieve high precision and low uncertainty already at small sample sizes (virtually less than 200 enumerated cells) and thus they minimize the allocated effort vs. the gained information. Accordingly to our observations, we provide recommendations about the metric selection and the optimal effort per sample to be allocated in phytoplankton monitoring plans. [ABSTRACT FROM AUTHOR]

Highlights • Low coherence for GES definitions in Mediterranean plankton communities was found. • Phytoplankton is a key element for assessment systems of MSFD and Regional Conventions. • GES targets are based only on Chlorophyll a thresholds in the Mediterranean so far. • Quantitative GES targets for zooplankton in Mediterranean exist only in Slovenia. • Gaps mostly focus on lack of thresholds and baselines for many biodiversity indicators. Abstract At present there is no consistent approach for the definition of Good Environmental Status (GES) and targets in the Mediterranean Sea, especially for Biodiversity Descriptors, according to the Article 12 of the Marine Strategy Framework Directive (MSFD). The use of plankton indicators in the Mediterranean Sea refers mostly to pelagic habitats in coastal waters and to case studies connected with environmental pressures, e.g. in the Adriatic, Aegean etc. The aim of this review is to study the existing biodiversity indicators for different plankton groups in order to compare GES definitions for the Biodiversity Descriptor and identify the relevant gaps and priority needs to improve coherence for the MSFD implementation across the Mediterranean. For these purposes, we focus on plankton indicators for phytoplankton, zooplankton and prokaryotes. Regional conventions (OSPAR, HELCOM, Barcelona and Bucharest Conventions) have long considered phytoplankton as a key element for integrated assessment systems. Phytoplankton biomass, community composition, abundance, frequency and intensity of blooms are used for such assessment purposes. Chlorophyll a still remains the most widely used indicator mostly thanks to its time saving, cost-effective and reproducible analytical methods that provide easily comparable datasets. Despite some integrated indices proposed for phytoplankton in the literature at the Mediterranean level, a number of constrains still prevent their wide use. Regarding zooplankton communities, commonly used indicators have a taxonomic base while recently size structure and biomass can provide a valuable index of zooplankton population dynamics and ecosystem production. Jellyfish blooms' occurrence and frequency are also considered important zooplankton indicators in specific areas, e.g. North Adriatic. Concerning the prokaryotes, so far MSFD takes into account only their pathogenic component. The revision of MSFD GES definitions shows that all Mediterranean MSs have defined GES at the Descriptor level (e.g. D1 Biodiversity), but our comparison of approaches shows a low level of coherence in GES related to pelagic habitats and plankton communities. Gaps mostly focus on the lack of thresholds and baselines for many biodiversity indicators, and on the scarcity of common and consistent methodological approaches for biodiversity assessment by the MSs. Suggestions to fill these gaps and inconsistencies among MSs include: integration of EU legislation and Regional Agreements and Conventions; targeting on priority species and habitats; testing of existing biodiversity indices with good performances in case studies; coordination and intercalibration actions for the establishment of threshold values and baselines; determination of common methodologies; undertaking of regular monitoring programs and impact assessment studies at regional and sub-regional levels. [ABSTRACT FROM AUTHOR]