The great environmental importance of wetlands is linked to the high biodiversity of flora and fauna they support, so that the international Ramsar Convention focused on these areas and highlighted the need to preserve them. The bacterial communities that thrive in these ecosystems play a key role in regulating the local biogeochemical processes and yet their distribution, abundance and dynamics are poorly known. This work is aimed to study the bacterial assemblages over a year long, to contribute to the understanding of the natural processes occurring in wetlands at variable salinity. The knowledge of bacterial groups, species or assemblages can provide a useful bioindicator for conservation and restoration efforts. Macchiatonda Natural Reserve (Santa Severa, Rome, Italy) is a relic ecosystem, once found along the entire Tyrrhenian coast. This wetland encompasses three coastal ponds with different salinity, where both peculiar vegetation and highly diverse migratory and resident avifauna can be found. This ancient system has been scarcely investigated and nothing is known about its microbial community. The molecular metagenomic analyses performed to investigate the salinity/bacterioplankton relationship, highlighted differences in the bacterial structure, between ponds and seasons. Analogous trends in SSCP profiles, Shannon Index, and bacterial composition (16S) were observed in the two saltier ponds, whereas the entire set of results was different for the less salty one. The species diversity in the three ponds varied according the salinity gradient, with the maximum diversity corresponding to a salt concentration range between 20 and 30. At higher and lower salinity, the microbial diversity lowers, according to the “ Intermediate Disturbance Hypothesis ” .
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