Macroinvertebrates are commonly applied for ecological investigations and as ecological indicators. However, the role of the sampling technique, effort and habitat on macroinvertebrate descriptors, diversity indices and ecological indicators in transitional water ecosystems is little known yet. This research aims to evaluate the influence of sampling techniques on macroinvertebrate assemblages and ecological indicators comparing box-corer and litterbag techniques, in prairie and unvegetated habitats. The experiment was conducted in a protected Mediterranean shallow lagoon dominated by marine water input. Three types of litterbags were prepared with: i. Phragmites australis dry leaves (terrestrial input); ii. Posidonia oceanica dry leaves (marine input), and iii. an equal mixture of both leaves. Three replicates of box-corer samples were collected in two sites per habitat, litterbags were submerged and retrieved after 30 days. Macroinvertebrate abundance, species richness, diversity indices and ecological indicators were measured and compared among sampling techniques and between habitats. Macroinvertebrate data was then pooled, analysed and compared to each single technique. Twenty-seven species were sampled overall, 4 species overlapped between box-corer and litterbags, 6 species (26%) were exclusive to the box-corer and 16 species (59%) were caught using only litterbags. Species diversity in litterbags was always higher than in box-corer, but macroinvertebrate assemblages were described better when using data pooled. In prairie, the ecological indicators varied significantly between the data pooled and separate sampling technique. Finally, this research highlights the relevance of using more than one sampling technique to obtain a better description of macroinvertebrate assemblages and the ecological status of Mediterranean lagoons.
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