Methods
Due to the large variety of seafloor types, it is necessary to define indicators and standardized methods that can effectively convey the status of benthic ecosystems (i.e. those associated to the sea-floor) and of their alteration by pressures from human activities. 

From the framework laid down by the D6 task group, only a selection of two Seafloor Integrity criteria were considered in the Commission Decision 2010/477/EU in consideration of the aspects covered by the other MSFD Descriptors. This streamlined approach established that the criteria and subordinate indicators to assess seafloor integrity were:

6.1. Physical damage, having regard to substrate characteristics

The main concern for management purposes is the magnitude of impacts of human activities on seafloor substrates structuring the benthic habitats. Among the substrate types, biogenic substrates, which are the most sensitive to physical disturbance, provide a range of functions that support benthic habitats and communities.

- Type, abundance, biomass and areal extent of relevant biogenic substrate (6.1.1)

- Extent of the seabed significantly affected by human activities for the different substrate types (6.1.2).

6.2. Condition of benthic community

The characteristics of the benthic community such as species composition, size composition and functional traits provide an important indication of the potential of the ecosystem to function well. Information on the structure and dynamics of communities is obtained, as appropriate, by measuring species diversity, productivity (abundance or biomass), tolerant or sensitive taxa and taxocene dominance and size composition of a community, reflected by the proportion of small and large individuals.

- Presence of particularly sensitive and/or tolerant species (6.2.1)

- Multi-metric indexes assessing benthic community condition and functionality, such as species diversity and richness, proportion of opportunistic to sensitive species (6.2.2)

- Proportion of biomass or number of individuals in the macrobenthos above some specified length/size (6.2.3)

- Parameters describing the characteristics (shape, slope and intercept) of the size spectrum of the benthic community (6.2.4).

A review of D6 methodological standards available through EU Directives, Regional Sea Conventions and ISO standards for the first MSFD cycle can be found in Piha & Zampoukas 2011 (pages 27 to 30)


Methods used in assessing GES under the WFD can also be often used in assessing GEnS under the MSFD.




Technical work is ongoing to establish a comprehensive and operational MSFD Methodological Standards framework for D6 (e.g., under WG GES).
Additionally, the DEVOTES FP7 project has recently developed a software tool to help selecting indicators for the MSFD: the Devotool. Among the list of scientific indicators compiled, several are potentially useful to assess environmental status under D6. This resource can be used as an additional source of information to help establishing methodological.
Pressures
Human activities induce different kinds of pressures that can affect the sea-floor. The main pressures that directly impact the state of the sea bottom are:
  • Coastal infrastructures (ports, defences against erosion, etc.) and offshore installations (oil and gas platforms, wind farms, etc.);
  • Offshore mining and sand extraction;
  • Release of dredged sludge;
  • Moorings;
  • Some fishing practices (trawling, dredging, etc.);
  • Aquaculture (unused fish feed, fish faeces, etc.);
  • Introduction of non-indigenous species (trough ballast water for instance);
  • Pollution (chemical pollution, litter);
  • Changes in riverine inputs (organic enrichment of particulate matter, etc.);
  • Sediment remobilization by fishing equipment (trawls, dredges);
  • Changes in freshwater riverine inputs as a consequence of damming and irrigation;
  • Changes in solid matter riverine inputs; and
  • Release of large quantities of warm (power plant cooling) or salty water (from desalination facilities)
The mapping and quantification of the pressures applied to the sea-floor is an essential part of assessing and monitoring its ecological status. Data of the distribution of human activities must be collated to estimate, for example, the proportion of the seabed significantly affected by human activities for the different substrate types.
Effects
The pressures listed above, acting in isolation or together, may impact the structure of benthic ecosystems. For instance, changes in species composition may be induced by the damage of large or fragile species or by changes in their functioning. Others may be associated to the stimulation of opportunistic or scavenging species that may profit from disturbance of the bottom and availability of dead organisms. 

Indicators concerning the state of the benthic ecosystems need to be based on the presence of particularly sensitive or tolerant species or habitats. More robustly, they can be indices calculated from several parameters such as the species diversity, species richness and the proportion of different species groups in benthic samples. 

A particular attention has to be paid to some remarkable habitats that, in spite of their reduced spatial extent, play an important role in marine ecosystems dynamics and biodiversity (e.g. biogenic reefs, cold-water corals, maerl beds). The distribution of these and other habitats may be mapped from geo-referenced data gathered by acoustic sonars and optical camera surveys. Repeated surveys are only practicable for some particular habitats distributed over small/discrete areas but they are fundamental to gather information on possible changes in habitat extent.