Microbial communities associated with two populations of the sponge Chondrilla nucula under present and projected climate conditions in the Aegean Sea

This data paper describes bacterial and fungal communities associated with the sponge Chondrilla nucula collected from two Eastern Mediterranean populations (North and South Aegean Sea) and maintained under controlled common-garden conditions simulating present and projected climate scenarios over a period of 3 months. Microbial composition was characterized using two complementary ribosomal marker approaches: Illumina MiSeq sequencing of the 16S rRNA gene for Bacteria and Oxford Nanopore (MinION) sequencing of a long 18S-ITS-28S rRNA fragment for Fungi. A total of 24 sponge libraries (3 climate conditions x 2 populations x 4 biological replicates) along with 6 control libraries (water from 3 experimental tanks, extraction and PCR blanks) were constructed for each group of microsymbionts. The resulting reads were processed using custom and publicly available bioinformatic pipelines and databases on a local high-performance computing facility, followed by initial taxonomic assignment. This dataset represents the first fungal community associated with C. nucula and the first bacterial community for this species from the Aegean Sea.