Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns.

Anoop Alex,Agostinho Antunes,Connie Lovejoy

doi:10.1371/journal.pone.0127455

Abstract

Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.

Highlights

Sponge microbial ecology is attaining momentum with the advancement of sequencing technology and the keen interest in unlocking the global sponge-associated microbial diversity
454 sequencing and quality sorting of the microbial communities associated with the sponges and seawater derived 84,199 sequence reads clustered at 97% identity into 686 unique operational taxonomic units (OTUs)
The total number of reads retrieved and OTUs from each sample are provided in S2 Fig. The highest number of OTUs was observed in the sponge Amphilectus fucorum (AMF), representing up to 370 OTUs and minimum of 29 OTUs from the sponge Cliona celata (CCL) (Fig 1)

Summary

Introduction

Sponge microbial ecology is attaining momentum with the advancement of sequencing technology and the keen interest in unlocking the global sponge-associated microbial diversity. The sponge-associated microorganisms can contribute to nearly 40% of the total sponge biomass [1] and may benefit the hosts with various functional roles. Culture-independent 16S rRNA (ribosomal RNA) gene based molecular techniques, such as Sanger sequence analyses derived from clone library [2,3,4], denaturing gradient gel electrophoresis [5], terminal restriction fragment length polymorphism [3,6] and culture-dependent isolation procedures [2,4] provided insight into the complex sponge microbial consortium. Apart from cataloging the microbial diversity, the potential pharmacological application of bioactive compounds isolated from the sponges and associated microbes further intensified the effort to understand the sponge-associated microbial world [10]. Sponge-associated microbes has been classified as photosynthetic bacteria [24], heterotrophic bacteria, archaea [25] and non-representative candidate phyla [26,27]

Methods

Results

Discussion

Conclusion