The sponge microbiome within the greater coral reef microbial metacommunity

Daniel F R Cleary,Esther Van Der Ent,Francisco J R C Coelho,Nicole J De Voogd,Marina R S Ferreira,Newton C M Gomes,Sumaitt Putchakarn,Thomas Swierts,Ana R M Polónia,Jinn-Pyng Ueng,Luis Carvalheiro,Yusheng M Huang

doi:10.1038/s41467-019-09537-8

Abstract

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.

Highlights

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity
We applied high-throughput 16S rRNA gene sequencing analysis to simultaneously assess the diversity of 216 prokaryote communities (Supplementary Data 1) from the following 14 biotopes: algae, chitons, stony corals, sea cucumber gut, sea cucumber mantle, sponge denizens, flatworms, nudibranch gut, nudibranch mantle, soft corals, sponges, sea urchins, seawater and sediment (Fig. 1)
We recorded 30,725 operational taxonomic unit (OTU) assigned to 68 phyla over 2,160,000 sequences

Summary

Introduction

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities These biotopes share a higher percentage and number of OTUs with sediment and are enriched in members of the phylum Planctomycetes. High diversity hosts include samples of algae, chitons, stony corals and the sea cucumber gut and mantle Samples from these hosts are compositionally similar, and have relatively high abundances of operational taxonomic units (OTUs) assigned to the phylum Planctomycetes and relatively high OTU richness and evenness. Prokaryote communities of this group share significantly more OTUs100 (OTUs with >100 sequences) with sediment (i.e. OTUs found in sediment but not seawater) than other biotopes. Sponges, nudibranchs, flatworms and sponge denizens have much fewer sediment prokaryotes OTUs100 and a concomitantly lower prokaryote richness, despite having a sometimes very high contribution of environmental OTUs100 to total OTUs100 richness

Methods

Results

Conclusion