| Summary: | The composition of prokaryotic communities was determined in the meso- and bathypelagic waters funneled through the Romanche Fracture Zone (RFZ, 2 degrees 7'S, 31 degrees 79'W to 0 degrees 6'N, 14 degrees 33'W) in the tropical Atlantic. Distinct water masses were identified based on their physical and chemical characteristics. The bacterial and archaeal communities were depth-stratified with a total of 116 and 25 operational taxonomic units (OTUs), respectively, distributed among the distinct water masses as revealed by terminal restriction fragment length polymorphism, and cloning and sequencing. The relative abundance of Thaumarchaeota, determined by catalyzed reporter deposition-fluorescence in situ hybridization, was significantly higher in deeper layers (Antarctic Bottom Water, AABW, > 4000 m depth), contributing up to 31% to the total prokaryotic community, than in the mesopelagic and lower euphotic layer. Although the contribution of SAR11 to bacterial abundance did not increase with depth, SAR202, SAR324, SAR406 and Alteromonas did increase with depth. Terminal restriction fragment length polymorphism analysis revealed successional changes in the bacterial and archaeal community composition of the North Atlantic Deep Water (NADW) with a passage time through the RFZ of c. 4 months but not in the under- and overlying water masses. Our results indicate that specific water masses harbor distinct bacterial and archaeal communities and that the prokaryotic community of the NADW undergoes successional changes in this conduit between the western and eastern Atlantic basin. Apparently, in the absence of major input of organic matter to specific deep-water masses, the indigenous prokaryotic community adapts to subtle physical and biogeochemical changes in the water mass within a time frame of weeks, similar to the reported seasonal changes in surface water prokaryotic communities.
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