Abstract
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.
Highlights
Polymetallic nodules occur over vast areas of the abyssal ocean floor (Ghosh & Mukhopadhyay, 2000) and are enriched in commercially valuable minerals such as manganese (Mn), cobalt (Co), copper (Cu), nickel (Ni), and rare-earth elements (Wegorzewski & Kuhn, 2014)
These data were normalized to 5,400 reads/sample to account for uneven sampling depth, and either this normalized operational taxonomic unit (OTU) table, or a table normalized to relative abundance, was used in subsequent analyses, except the differential abundance analysis in which the full dataset was used and alpha diversity analyses in which samples were collapsed by sample type and the dataset was subsampled randomly multiple times at different depths, with a maximum depth of 100,100 sequences
After rarefaction, 112,926 distinct prokaryotic OTUs were recovered from the three types of samples, with 74% of these amplicons deriving from bacteria, 24% from archaea, and an additional 2% that could not be confidently assigned at the Domain level
Summary
Polymetallic (i.e., manganese) nodules occur over vast areas of the abyssal ocean floor (Ghosh & Mukhopadhyay, 2000) and are enriched in commercially valuable minerals such as manganese (Mn), cobalt (Co), copper (Cu), nickel (Ni), and rare-earth elements (Wegorzewski & Kuhn, 2014). We present findings of the bacterial, archaeal, and microeukaryotic communities associated with a polymetallic nodule field based on amplification and sequencing of rRNA genes. These analyses included 75 sediment samples, 24 water column samples, and 20 individual nodules from 11 stations randomly distributed over a 30 × 30 km stratum (AB-01; Table 1, Figure 1a) within the United (a). Our results reveal for the first time a diverse nodule eukaryotic community harboring OTUs assigned to the Sar, Opisthokonta, and Cryptophyceae lineages, as well as a core prokaryotic nodule community with OTUs found in nodules collected 3000 to >9000 km from our study site These results suggest polymetallic nodules may harbor a persistent and stable microbiome
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