Sponge and seawater metagenomes of Fernando de Noronha archipelago

13 marine sponge and 18 seawater samples collected at 4 different locations inside and outside submarine caves and burrows at depths ranging from 3-20 m are included in the study. 16S rRNA genes were amplified using the universal primers 515F and 806R for both bacteria and archaea. The goals of the study were to characterize the understudied cave-dwelling sponge microbiome from regions in the Fernando de Noronha archipelago, Northeast Brazil.