The central Mediterranean Sea is among the most oligotrophic habitats in the marine environment. In this study, we investigated the abundance, diversity and activity of prokaryoplankton in the water column (25–3000-m depth) at Station Vector (Tyrrhenian Sea, 39°32.050′ N; 13°22.280′ E). This specific water column consists of three different water masses (Modified Atlantic Water (MAW), Levantine Intermediate Water (LIW) and Tyrrhenian Deep Water (TDW), possessing a typical stratification of the Central Mediterranean basin. CARD-FISH showed that the metabolically-active fraction of bacterial populations exceeded the archaeal fraction along the whole water column, except at the deepest water masses. 16S rDNA and 16S rRNA clone libraries obtained from each type of water mass were used to analyse the prokaryoplankton community structure and to distinguish between active and “less active” microbial fractions. Our results showed that the rRNA-derived bacterial libraries seemed to be more depth specific compared to 16S rDNA-derived counterparts. Major differences were detected between the active fractions of bacterioplankton thriving in photic (25 m, MAW) and aphotic layers (500–3000 m, LIW and TDW respectively), whereas no statistically-significant differences were detected within the deep, aphotic layers (500–3000 m, LIW and TDW). Archaeal communities possessed more depth-specific distribution patterns with both total and active fractions showing depth stratification. Cyanobacteria and Marine Group II MAGII of Euryarchaea dominated the MAW prokaryoplankton. A notable fraction of Geitlerinema-related cyanobacteria
was detected among the metabolically-active bacterial population recovered from the mesopelagic (500 m, LIW) aphotic layer, which is indicative of their mixotrophic behaviour. Heterotrophic Gammaproteobacteria and members of Marine Group 1.1a and the PSL12-related ALOHA group of Thaumarchaeota were both abundant in the aphotic layers (both LIW and TDW). Discrepancies observed between 16S rDNA- and 16S rRNA-based libraries are most likely linked to different physiological states of the prokaryoplankton community members recovered from different layers. Taking into account the relative homogeneity of the main physicochemical parameters throughout the whole water column, light and energy source are likely the most relevant environmental variables shaping microbial biodiversity through the Station Vector water column.
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