Dataset Information

Host population genetics and biogeography structure the microbiome of the sponge Cliona delitrix.

ABSTRACT: Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted by the excavating sponge Cliona delitrix. A total of 53 samples, previously used to demarcate the population genetic structure of C. delitrix, were selected from two locations in the Caribbean Sea and from eight locations across the reefs of Florida and the Bahamas. Microbial community diversity and composition were measured using Illumina-based high-throughput sequencing of the 16S rRNA V4 region and related to host population structure and geographic distribution. Most operational taxonomic units (OTUs) specific to Cliona delitrix microbiomes were rare, while other OTUs were shared with congeneric hosts. Across a large regional scale (>1,000 km), geographic distance was associated with considerable variability of the sponge microbiome, suggesting a distance-decay relationship, but little impact over smaller spatial scales (<300 km) was observed. Host population structure had a moderate effect on the structure of these microbial communities, regardless of geographic distance. These results support the interplay between geographic, environmental, and host factors as forces determining the community structure of microbiomes associated with C. delitrix. Moreover, these data suggest that the mechanisms of host regulation can be observed at the population genetic scale, prior to the onset of speciation.

SUBMITTER: Easson CG

PROVIDER: S-EPMC7042757 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Host population genetics and biogeography structure the microbiome of the sponge <i>Cliona delitrix</i>.

Easson Cole G CG Chaves-Fonnegra Andia A Thacker Robert W RW Lopez Jose V JV

Ecology and evolution 20200124 4

Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted ...[more]

PMID: 32128133

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Project description:BACKGROUND:We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbiodinium-host interactions involves cnidarian partners. To fully and broadly understand the conditions that permit Symbiodinium to procure intracellular residency, we must explore hosts from different taxa to help uncover universal cellular and genetic strategies for invading and persisting in host cells. Here, we present data from gene expression analyses involving the bioeroding sponge Cliona varians that harbors Clade G Symbiodinium. RESULTS:Patterns of differential gene expression from distinct symbiont states ("normal", "reinfected", and "aposymbiotic") of the sponge host are presented based on two comparative approaches (transcriptome sequencing and suppressive subtractive hybridization (SSH)). Transcriptomic profiles were different when reinfected tissue was compared to normal and aposymbiotic tissue. We characterized a set of 40 genes drawn from a pool of differentially expressed genes in "reinfected" tissue compared to "aposymbiotic" tissue via SSH. As proof of concept, we determined whether some of the differentially expressed genes identified above could be monitored in sponges grown under ecologically realistic field conditions. We allowed aposymbiotic sponge tissue to become re-populated by natural pools of Symbiodinium in shallow water flats in the Florida Keys, and we analyzed gene expression profiles for two genes found to be increased in expression in "reinfected" tissue in both the transcriptome and via SSH. These experiments highlighted the experimental tractability of C. varians to explore with precision the genetic events that occur upon establishment of the symbiosis. We briefly discuss lab- and field-based experimental approaches that promise to offer insights into the co-opted genetic networks that may modulate uptake and regulation of Symbiondinium populations in hospite. CONCLUSIONS:This work provides a sponge transcriptome, and a database of putative genes and genetic pathways that may be involved in Symbiodinium interactions. The relative patterns of gene expression observed in these experiments will need to be evaluated on a gene-by-gene basis in controlled and natural re-infection experiments. We argue that sponges offer particularly useful characteristics for discerning essential dimensions of the Symbiodinium niche.

Project description:Characterizing the gut microbiome in the healthy population is the first step in elucidating its associations with host health conditions. Populations with different diet patterns, lifestyles, and genetic backgrounds harbor different gut microbes. In this study, we characterized the gut microbiome of 890 healthy Koreans using 16S rRNA sequencing. The Korean population harbored a relatively large fraction of the Prevotella enterotype and presented a distinctive gut microbiome, compared to that in the populations of other countries. Additionally, we determined the clusters of cooccurring microbes that were quantitatively correlated with each other. We found that microbe composition of the gut was strongly associated with age. We identified that the abundance of members of Bacteroidia and Clostridia differed with the host dietary patterns, body mass index, and stool frequency. The gut microbiome data obtained in this study would be an important resource for future studies addressing microbial contributions in health and disease. IMPORTANCE Comparing the gut microbiomes of healthy controls and disease patients showed that the composition of the gut microbiome is associated with various host health conditions. The gut microbiome in healthy Western populations is well characterized, while that of non-Western populations, with different diet patterns, lifestyles, and genetic backgrounds, is not clearly defined. In this study, we characterized the microbiome of 890 healthy Korean individuals using 16S rRNA sequencing and found that Koreans have a gut microbiome different from that in the individuals of neighboring countries. The members of Bacteroidetes and Firmicutes cooccurred and were quantitatively associated with each other. Additionally, we found that the gut microbial composition is strongly associated with the host's age. The microbiome data presented here represent the gut microbiome of a healthy Korean population and could be used to unveil gut microbiome-associated host conditions in this population.

Dataset Information

Host population genetics and biogeography structure the microbiome of the sponge Cliona delitrix.

Publications

Host population genetics and biogeography structure the microbiome of the sponge <i>Cliona delitrix</i>.

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