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The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfidic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor affecting the microbial assemblages of the blue hole and surrounding open sea waters, and significantly explained 44.7% of the total variation, followed by silicate, temperature, sulfide, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll  a . We identified a bloom of  Alteromonas  (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll  a  peak in the blue hole. Genomic potential for nitrate reduction of  Alteromonas  might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrification, and sulfur-oxidization were enriched at nitrate/nitrite-sulfide transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera  Sulfurimonas  and  Arcobacter , and Chlorobi harbored genes for sulfur-driven denitrification process that mediated nitrogen loss and sulfide removal. In the anoxic bottom seawater (100-300 m), high levels of sulfate reducers and dissimilatory sulfite reductase gene ( dsr  A ) potentially created a sulfidic zone of ~200 m thickness. Our findings suggest that in the oligotrophic Sansha Yongle Blue Hole, O 2  deficiency promotes nitrogen- and sulfur-cycling processes mediated by metabolically versatile microbials.

Microbial Diversity and Metabolic Potential in the Stratified Sansha Yongle Blue Hole in the South China Sea