A major source of complexity in marine ecosystem monitoring is represented by the fact that ecosystem processes occurring across different spatial and temporal scales. The implementation of the monitoring strategies applied in accordance to Marine Framework Strategy Directive (MFSD, 2008/56/EC) is a step-by-step process, which should be focus on the potential of scale dependence in the observed dynamics and should be able to integrate the effect of mediating factors operating at different scale levels. Nevertheless, the correct definition of monitoring efforts for each indicator needs to reach a well-defined knowledge on the actual assessment of the “object” of monitoring including ranges of natural variability in terms of spatial and temporal natural fluctuations. Unluckily natural fluctuations are not yet well defined in marine environments for all of the MSFD indicators. For these reasons the achievement of MSFD goals could be severely affected by the lack of knowledge which led to the lack of clear and rationale criteria on the basis of which to align and cope the scale of the assessment with the ecosystem natural fluctuations. Hereby we address the design of monitoring programmes concerning water column and seabed habitats integrity indicators (Descriptors D1, D5, D6) by discussing spatial and temporal extent of monitoring based on their scales of natural variation. The multiple layer approach developed on mesoscales could allow reducing mistakes due to sampling and methodological limits and could allow reducing problems ranging within the comprehension of mechanisms to the anticipation of consequences. The opportune mesoscale is dependent on the indicator considered and range within 0.5 – 100 km for the spatial scale and from 0.2 to 12 months for the temporal scale.
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