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. 2019 Nov;88(11):1684-1695.
doi: 10.1111/1365-2656.13065. Epub 2019 Sep 3.

Host genetics and geography influence microbiome composition in the sponge Ircinia campana

Sarah M Griffiths  1 , Rachael E Antwis  2 , Luca Lenzi  3 , Anita Lucaci  3 , Donald C Behringer  4   5 , Mark J Butler 4th  6 , Richard F Preziosi  1
Affiliations

Host genetics and geography influence microbiome composition in the sponge Ircinia campana

Sarah M Griffiths et al. J Anim Ecol. 2019 Nov.

Abstract

Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.

Keywords: Porifera; bacteria; core microbiome; eco-evolutionary dynamics; genetic diversity; host-microbe interactions; microsatellites.

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Figures

Figure 1
Figure 1
Principal coordinates analysis (PCoA) showing Euclidean genetic distances among Ircinia campana individuals at Long Key and Kemp Channel
Figure 2
Figure 2
Principle coordinates analysis (PCoA) showing Bray–Curtis distances among microbiomes of Ircinia campana from Long Key and Kemp Channel
Figure 3
Figure 3
Scatter plot with regression lines showing correlations between pairwise host Euclidean genetic distances (using nine microsatellite genotypes) and microbial community Chao1 distances (alpha diversity) in Ircinia campana at (a) Long Key, and (b) Kemp Channel, and host genetic Euclidean distances and microbial community Jensen–Shannon divergence values (beta diversity) at (c) Long Key, and (d) Kemp Channel. Shaded areas show 95% confidence intervals
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References

    1. Alberto, F. (2009). MsatAllele_1. 0: An R package to visualize the binning of microsatellite alleles. Journal of Heredity, 100(3), 394–397. 10.1093/jhered/esn110 - DOI - PubMed
    1. Altschul, S. F. , Gish, W. , Miller, W. , Myers, E. W. , & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Antwis, R. E. , Griffiths, S. M. , Harrison, X. A. , Aranega‐Bou, P. , Arce, A. , Bettridge, A. S. , … Sutherland, W. J. (2017). Fifty important research questions in microbial ecology. FEMS Microbiology Ecology, 93(5), 10.1093/femsec/fix044 - DOI - PubMed
    1. Astudillo‐García, C. , Bell, J. J. , Webster, N. S. , Glasl, B. , Jompa, J. , Montoya, J. M. , & Taylor, M. W. (2017). Evaluating the core microbiota in complex communities: A systematic investigation. Environmental Microbiology, 19(4), 1450–1462. 10.1111/1462-2920.13647 - DOI - PubMed
    1. Bankevich, A. , Nurk, S. , Antipov, D. , Gurevich, A. A. , Dvorkin, M. , Kulikov, A. S. , … Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single‐cell sequencing. Journal of Computational Biology, 19(5), 455–477. 10.1089/cmb.2012.0021 - DOI - PMC - PubMed

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