Concentrated seabed deposits of polymetallic nodules, which are rich in economically valuable metals (e.g., copper, nickel, cobalt, manganese), occur over vast areas of the abyssal Pacific Ocean floor. Little is currently known about the diversity of microorganisms inhabiting abyssal habitats. In this study, sediment, nodule, and water column samples were collected from the Clarion-Clipperton Zone of the Eastern North Pacific. The diversities of prokaryote and microeukaryote communities associated with these habitats were examined. Microbial community composition and diversity varied with habitat type, water column depth, and sediment horizon. Thaumarchaeota were relatively enriched in the sediments and nodules compared to the water column, whereas Gammaproteobacteria were the most abundant sequences associated with nodules. Among the Eukaryota, rRNA genes belonging to the Cryptomonadales were relatively most abundant among organisms associated with nodules, whereas rRNA gene sequences deriving from members of the Alveolata were relatively enriched in sediments and the water column. Nine operational taxonomic unit (OTU)s were identified that occur in all nodules in this dataset, as well as all nodules found in a study 3000-9000 km from our site. Microbial communities in the sediments had the highest diversity, followed by nodules, and then by the water column with <1/3 the number of OTUs as in the sediments.

Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.