Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

Abstract

Marine sponges are well known for their associations with highly diverse, yet very specific and often highly similar microbiota. The aim of this study was to identify potential bacterial sub-populations in relation to sponge phylogeny and sampling sites and to define the core bacterial community. 16S ribosomal RNA gene amplicon pyrosequencing was applied to 32 sponge species from eight locations around the world's oceans, thereby generating 2567 operational taxonomic units (OTUs at the 97% sequence similarity level) in total and up to 364 different OTUs per sponge species. The taxonomic richness detected in this study comprised 25 bacterial phyla with Proteobacteria, Chloroflexi and Poribacteria being most diverse in sponges. Among these phyla were nine candidate phyla, six of them found for the first time in sponges. Similarity comparison of bacterial communities revealed no correlation with host phylogeny but a tropical sub-population in that tropical sponges have more similar bacterial communities to each other than to subtropical sponges. A minimal core bacterial community consisting of very few OTUs (97%, 95% and 90%) was found. These microbes have a global distribution and are probably acquired via environmental transmission. In contrast, a large species-specific bacterial community was detected, which is represented by OTUs present in only a single sponge species. The species-specific bacterial community is probably mainly vertically transmitted. It is proposed that different sponges contain different bacterial species, however, these bacteria are still closely related to each other explaining the observed similarity of bacterial communities in sponges in this and previous studies. This global analysis represents the most comprehensive study of bacterial symbionts in sponges to date and provides novel insights into the complex structure of these unique associations.

Evidence for rapid, tide-related shifts in the microbiome of the coral Coelastrea aspera

“…The core microbiome of sponges has also recently been characterized and, again, core members depended on the cutoff used (Schmitt et al 2012). At 97% cutoff only three core phylotypes were identified, increasing to eight when a 95% cutoff was used, and 18 at 90% (Schmitt et al 2012). In this study, only five phylotypes were identified as core using the 90% cutoff (Pseudomonas, two cyanobacteria, Propionibacterium and Rothia).…”

“…However, in the same study there was no single abundant bacterial species (defined as [0.5% of the community) shared by all 154 individuals studied. The core microbiome of sponges has also recently been characterized and, again, core members depended on the cutoff used (Schmitt et al 2012). At 97% cutoff only three core phylotypes were identified, increasing to eight when a 95% cutoff was used, and 18 at 90% (Schmitt et al 2012).…”

Down under the tunic: bacterial biodiversity hotspots and widespread ammonia-oxidizing archaea in coral reef ascidians

“…Encompassing 3321 unique OTU 0.03 from 19 described bacterial phyla, 14 candidate bacterial phyla and 3 described archaeal phyla, the ascidian microbiota exhibited comparable diversity to the rich microbiota associated with marine sponges (Schmitt et al, 2012) and corals (Sunagawa et al, 2010) and indicates that the ascidian tunic represents a previously unrecognized hotspot for marine microbial diversity. Visualization of microbial cells by transmission electron microscopy confirmed the presence of microbes in the ascidian tunic and was consistent with results from 16S rRNA gene tag pyrosequencing, for example, the prevalence of cyanobacterial OTUs (450% of sequence reads) and cyanobacterial cells encased in a fiber network in Pycnoclavella sp.…”

“…Sub-sampling of sequence pools from samples with greater than 2000 reads were performed in the mothur software package to standardize sampling effort and determine its effect on diversity estimates. Host-specificity of the ascidian microbiota was assessed by partitioning OTUs into core (present in 470% of host species), variable (present in at least two host species) and specific (present in a single host species) groups (sensu Schmitt et al, 2012). To broaden the analysis of the specificity of the ascidian microbiota, abundant ascidian-associated OTUs (i.e., those represented by 4100 total sequence reads) were compared to sequences in the GenBank database using a nucleotide-nucleotide BLAST search (Altschul et al, 1990).…”

Bacterial Diversity in the Guts of Sea Cucumbers (Apostichopus japonicus) and Shrimps (Litopenaeus vannamei) Investigated with Tag-Encoded 454 Pyrosequencing of 16S rRNA Genes

“…이는 해삼과 새우에서 미분류군이 많은 이 유를 설명해 준다. 실제로 해면과 같은 해양 무척추 동물의 경우 에도 기존에 분류학적으로 알려지지 않은 많은 수의 서열들이 발견되고 있다 (Schmitt et al, 2012). 예를 들어 "Poribacteria" 와 같은 그룹은 해면에서만 특이적으로 발견되는 문으로서 아직 까지 순수 배양이 된 균주가 없기 때문에 후보 문(candidate phylum)으로만 정의 되어 있다 (Fieseler et al, 2004 …”