Host-specificity among abundant and rare taxa in the sponge microbiome

Abstract

Microbial communities have a key role in the physiology of the sponge host, and it is therefore essential to understand the stability and specificity of sponge-symbiont associations. Host-specific bacterial associations spanning large geographic distance are widely acknowledged in sponges. However, the full spectrum of specificity remains unclear. In particular, it is not known whether closely related sponges host similar or very different microbiota over wide bathymetric and geographic gradients, and whether specific associations extend to the rare members of the sponge microbiome. Using the ultra-deep Illumina sequencing technology, we conducted a comparison of sponge bacterial communities in seven closely related Hexadella species with a well-resolved host phylogeny, as well as of a distantly related sponge Mycale. These samples spanned unprecedentedly large bathymetric (15-960 m) gradients and varying European locations. In addition, this study included a bacterial community analysis of the local background seawater for both Mycale and the widespread deep-sea taxa Hexadella cf. dedritifera. We observed a striking diversity of microbes associated with the sponges, spanning 47 bacterial phyla. The data did not reveal any Hexadella microbiota co-speciation pattern, but confirmed sponge-specific and species-specific host-bacteria associations, even within extremely low abundant taxa. Oligotyping analysis also revealed differential enrichment preferences of closely related Nitrospira members in closely related sponges species. Overall, these results demonstrate highly diverse, remarkably specific and stable spongebacteria associations that extend to members of the rare biosphere at a very fine phylogenetic scale, over significant geographic and bathymetric gradients.

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume

“…Bacterial communities were analyzed using 454 pyrosequencing of the V6V4 region of the bacterial 16S rRNA gene. Dates of sampling, specific water depth and locations are given in Table 1. virulent and nonpathogenic microorganisms (Eren et al, 2011), host-specific fecal-indicator bacteria (McLellan et al, 2013), marine SAR11 oligotypes and host-specificity in spongehosted microbial communities (Reveillaud et al, 2014). Importantly, the method is immune to complications originating from the occurrence of multiple copies of the 16S rRNA gene.…”

Population dynamics and diversity of Synechococcus on the New England Shelf

“…This region was amplified for each environmental MVCO sample in two successive PCR reactions. Reactions were performed in triplicate, each containing 5-20 ng of DNA template, 0.2 µM unfused V6 amplification primers (967F and 1046R, [86]), 1 unit of Platinum R Taq DNA Polymerase High Fidelity (Invitrogen), 2 mM MgSO 4 (Invitrogen), and 0.2 mM dNTPs (Bioworld) in a total 33 µL volume. Reactions were performed on a GeneAmp PCR System 9700 thermocycler (Applied Biosystems) with the following conditions: 94 C for 3 min; followed by 25 cycles of 30 sec at 94 C, 45 sec at 60 C, and 1 min at 72 C; with a final extension step of 72 C for 2 min.…”

New Insights into Microbial Ecology through Subtle Nucleotide Variation

“…Doing so not only allows finer representation of the microbial diversity in a wide range of ecosystems, but also improves the ecological signal for downstream analyses that aim to infer correlations (McLellan and Eren, 2014;Reveillaud et al, 2014;Eren et al, 2015;Kleindienst et al, 2015).…”