Metagenomic analysis of marine Sponges-associated microbiome isolated from Chuuk lagoon, Micronesia

Abstract

Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. By filtering extensive volumes of seawater up to thousands of liters per kg sponge daily they take in food bacteria, but also potential pathogens, toxins, and physical stress factors. Marine sponges often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass and are found at densities exceeding 109 microbial cells per cubic centimeter of sponge tissue. Marine sponges and their microbiomes boast an impressive metabolic and chemical repertoire that not only contributes to their nutritional ecology but also has elicited the interest of the pharmaceutical industry owing to their production of biologically active compounds such as PKS and NRPS. Here, we analyzed the sponge-derived microbiome and tried to obtain PKS or NRPS-related gene clusters through high throughput sequencing analysis. Four different sponge samples (194CH01, 194CH03, 194CH07, and 194CH09) were collected from Chuuk lagoon, Federated State of Micronesia, and subjected to a culture-independent microbial cell collection. Metagenome DNA was extracted from the cells both of the using kit and manual DNA extraction, and then data sets were obtained by Illumina MiSeq sequencing followed by untargeted metagenomic binning. Eleven, ten, eighteen, and seventeen bacteria phyla were detected from the sponge samples in 194CH01, 194CH03, 194CH07, and 194CH09, respectively, by phylogenetic analyses of the 16S rRNA gene libraries. The 194CH-07 DNA sample showed up to 98% of the Bacteria-derived sequence. The most abundant phylum in the 194CH07 sponge library was the Proteobacteria, with the majority of these sequences being from the γ-Proteobacteria. Obtained DNA fragments were assembled into 368,388 contigs at a total size of 967 Mbp with the 3.6 Mbp of maximum contig size. A total of 938,641 protein-coding genes were predicted, comprising 383,955 COG assigned genes and 266,066 of them were assigned to a putative function based on the subsystem database. 189 PKS related gene clusters were detected from AntiSMASH search tool, however, the gene cluster possessing complete module was not detected.