Benthic prokaryotic communities, utmost important for wetlands and marine environments functioning, are influenced by physical-chemical parameters and interactions with other communities, especially micro-eukaryotes and meiofauna. Thus, a holistic view of the benthic community is necessary to fully understand their organization and functioning. This study assesses the implementation of a comprehensive view, using mock communities and environmental samples. A DNA extraction strategy combining two procedures is proposed: one to obtain DNA from micro-organisms, using 0.25 g of sediment, and the other from meiofauna, using 0.25 g of sieving refluxes from 5 g of sediment. Three conditions were considered to create mock communities: (i) varying eukaryotes’ abundance, (ii) adding meiofauna from salted or freshwater wetlands, and (iii) including or not a sediment matrix. Most organisms composing the mock communities were detected, except a filamentous cyanobacteria. All mock communities showed similar composition indicating that sediment did not affect the DNA extraction. This result also demonstrated that sieving, necessary to enrich meiofauna from sediment, does not significantly affect any of the communities. For the environmental samples investigated, most of the taxa usually described in the literature were retrieved in the salted, brackish and freshwater marshes sediment. The proposed approach was successful in analysing organisms from the three domains of life in a unique environmental sample, providing a holistic view of the benthic community. Furthermore, the significant differences observed between samples from the three different marshes, indicated that our approach can be used for conducting successful ecological studies, especially useful for understanding benthic communities’ interactions.
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