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Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes

  • McFall-Ngai, M. et al. Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U.S.A. 110, 3229–3236 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Hammer, T. J., Sanders, J. G. & Fierer, N. Not all animals need a microbiome. FEMS Microbiol. Lett. 366, fnz117 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Griffiths, S. M. et al. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J. Anim. Ecol. 88, 1684–1695 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Coleman-Derr, D. et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. New Phytol. 209, 798–811 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Marzinelli, E. M. et al. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography. Environ. Microbiol. 17, 4078–4088 (2015).

    Article 
    PubMed 

    Google Scholar 

  • Wang, L., English, M. K., Tomas, F. & Mueller, R. S. Recovery and community succession of the Zostera marina Rhizobiome after transplantation. bioRxiv https://doi.org/10.1101/2020.04.20.052357 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Copeland, J. K., Yuan, L., Layeghifard, M., Wang, P. W. & Guttman, D. S. Seasonal community succession of the phyllosphere microbiome. Mol. Plant. Microbe. Interact. 28, 274–285 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Shi, S. et al. Successional trajectories of rhizosphere bacterial communities over consecutive seasons. MBio 6, e00746 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Shade, A., McManus, P. S. & Handelsman, J. Unexpected diversity during community succession in the apple flower microbiome. MBio 4, e00602 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Avena, C. V. et al. Deconstructing the bat skin microbiome: Influences of the host and the environment. Front. Microbiol. 7, 1753 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar 

  • Glasl, B., Smith, C. E., Bourne, D. G. & Webster, N. S. Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7, e6377 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Weigel, B. L. & Erwin, P. M. Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila. Sci. Rep. 7, 43247 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fuhrman, J. A., Cram, J. A. & Needham, D. M. Marine microbial community dynamics and their ecological interpretation. Nat. Rev. Microbiol. 13, 133–146 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Ziegler, M. et al. Coral bacterial community structure responds to environmental change in a host-specific manner. Nat. Commun. 10, 3092 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wagner, M. R. et al. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7, 12151 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kraft, N. J. B. et al. Community assembly, coexistence and the environmental filtering metaphor. Funct. Ecol. 29, 592–599 (2015).

    Article 

    Google Scholar 

  • Weiher, E. & Keddy, P. A. The assembly of experimental wetland plant communities. Oikos 73, 323–335 (1995).

    Article 

    Google Scholar 

  • Cavender-Bares, J., Kitajima, K. & Bazzaz, F. A. Multiple trait associations in relation to habitat differentiation among 17 Floridian oak species. Ecol. Monogr. 74, 635–662 (2004).

    Article 

    Google Scholar 

  • Cavender-Bares, J., Ackerly, D. D., Baum, D. A. & Bazzaz, F. A. Phylogenetic overdispersion in Floridian oak communities. Am. Nat. 163, 823–843 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Webb, C. O. Exploring the Phylogenetic structure of ecological communities: An example for rain forest trees. Am. Nat. 156, 145–155 (2000).

    Article 
    PubMed 

    Google Scholar 

  • Webb, C. O., Ackerly, D. D., McPeek, M. A. & Donoghue, M. J. Phylogenies and community ecology. Annu. Rev. Ecol. Syst. 33, 475–505 (2002).

    Article 

    Google Scholar 

  • Kembel, S. W. et al. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc. Natl. Acad. Sci. U.S.A. 111, 13715–13720 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S. & Thomas, T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U.S.A. 108, 14288–14293 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Martiny, J. B. H., Jones, S. E., Lennon, J. T. & Martiny, A. C. Microbiomes in light of traits: A phylogenetic perspective. Science https://doi.org/10.1126/science.aac9323 (2015).

    Article 
    PubMed 

    Google Scholar 

  • Goberna, M. & Verdú, M. Predicting microbial traits with phylogenies. ISME J. 10, 959–967 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Duarte, C. M. The future of seagrass meadows. Environ. Conserv. 29, 192–206 (2002).

    Article 

    Google Scholar 

  • Fonseca, M. S., Fisher, J. S., Zieman, J. C. & Thayer, G. W. Influence of the seagrass, Zostera marina L., on current flow. Estuar. Coast. Shelf Sci. 15, 351–364 (1982).

    Article 
    ADS 

    Google Scholar 

  • Fonseca, M. S., Kenworthy, W. J. & Thayer, G. W. A low cost transplanting procedure for sediment stabilization and habitat development using eelgrass (Zostera marina). Wetlands 2, 138–151 (1982).

    Article 

    Google Scholar 

  • Moore, K. A. & Short, F. T. Zostera: Biology, ecology, and management. In Seagrasses: Biology, ecology and conservation (eds Larkum, A. W. D. et al.) 361–386 (Springer, 2006).

    Google Scholar 

  • Fahimipour, A. K. et al. Global-scale structure of the eelgrass microbiome. Appl. Environ. Microbiol. 83, e03391-16 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bengtsson, M. M. et al. Eelgrass leaf surface microbiomes are locally variable and highly correlated with epibiotic eukaryotes. Front. Microbiol. 8, 1312 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cúcio, C., Engelen, A. H., Costa, R. & Muyzer, G. Rhizosphere microbiomes of European + seagrasses are selected by the plant, but are not species specific. Front. Microbiol. 7, 440 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schenck, F. R., DuBois, K., Kardish, M. R., Stachowicz, J. J. & Hughes, A. R. The effect of warming on seagrass wasting disease depends on host genotypic identity and diversity. Ecology e3959 (2022).

  • Beatty, D. S. et al. Predictable changes in eelgrass microbiomes with increasing wasting disease prevalence across 23° latitude in the Northeastern Pacific. mSystems 7, e0022422 (2022).

    Article 
    PubMed 

    Google Scholar 

  • Hughes, A. R., Stachowicz, J. J. & Williams, S. L. Morphological and physiological variation among seagrass (Zostera marina) genotypes. Oecologia 159, 725–733 (2009).

    Article 
    ADS 
    PubMed 

    Google Scholar 

  • Randall Hughes, A. & Stachowicz, J. J. Seagrass genotypic diversity increases disturbance response via complementarity and dominance. J. Ecol. 99, 445–453 (2010).

    Google Scholar 

  • Kamel, S. J., Hughes, A. R., Grosberg, R. K. & Stachowicz, J. J. Fine-scale genetic structure and relatedness in the eelgrass Zostera marina. Mar. Ecol. Prog. Ser. 447, 127–137 (2012).

    Article 
    ADS 

    Google Scholar 

  • Abbott, J. M., DuBois, K., Grosberg, R. K., Williams, S. L. & Stachowicz, J. J. Genetic distance predicts trait differentiation at the subpopulation but not the individual level in eelgrass Zostera marina. Ecol. Evol. 8, 7476–7489 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Sand-Jensen, K. Biomass, net production and growth dynamics in an eelgrass (Zostera marina L.) population in Vellerup Vig, Denmark. Ophelia 14, 185–201 (1975).

    Article 

    Google Scholar 

  • Vacher, C. et al. The phyllosphere: Microbial jungle at the plant-climate interface. Annu. Rev. Ecol. Evol. Syst. 47, 1–24 (2016).

    Article 

    Google Scholar 

  • Miazaki, A. S., Gastauer, M. & Meira-Neto, J. A. A. Environmental severity promotes phylogenetic clustering in campo rupestre vegetation. Acta Bot. Brasilica 29, 561–566 (2015).

    Article 

    Google Scholar 

  • DuBois, K., Williams, S. L. & Stachowicz, J. J. Previous exposure mediates the response of eelgrass to future warming via clonal transgenerational plasticity. Ecology 101, e03169 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Rüger, L. et al. Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.). Front. Microbiol. 12, 614501 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fitzpatrick, C. R. et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl. Acad. Sci. U.S.A. 115, E1157–E1165 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fitzgerald, D. B., Winemiller, K. O., Sabaj Pérez, M. H. & Sousa, L. M. Seasonal changes in the assembly mechanisms structuring tropical fish communities. Ecology 98, 21–31 (2017).

    Article 
    PubMed 

    Google Scholar 

  • Campbell, A. H., Marzinelli, E. M., Gelber, J. & Steinberg, P. D. Spatial variability of microbial assemblages associated with a dominant habitat-forming seaweed. Front. Microbiol. 6, 230 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Eriander, L., Infantes, E., Olofsson, M., Olsen, J. L. & Moksnes, P.-O. Assessing methods for restoration of eelgrass (Zostera marina L.) in a cold temperate region. J. Exp. Mar. Bio. Ecol. 479, 76–88 (2016).

    Article 

    Google Scholar 

  • Zhou, Y. et al. Restoring eelgrass (Zostera marina L.) habitats using a simple and effective transplanting technique. PLoS ONE 9, e92982 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Galushko, A. & Kuever, J. Desulfocapsaceae. Bergey’s Manual of Systematics of Archaea and Bacteria 1–6 Preprint at https://doi.org/10.1002/9781118960608.fbm00332 (2021).

  • Waite, D. W. et al. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int. J. Syst. Evol. Microbiol. 70, 5972–6016 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Knoblauch, C., Sahm, K. & Jørgensen, B. B. Psychrophilic sulfate-reducing bacteria isolated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov.. Int. J. Syst. Bacteriol. 49 Pt 4, 1631–1643 (1999).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Isaksen, M. F. & Teske, A. Desulforhopalus vacuolatus gen. nov., sp. nov., a new moderately psychrophilic sulfate-reducing bacterium with gas vacuoles isolated from a temperate estuary. Arch. Microbiol. 166, 160–168 (1996).

    Article 
    CAS 

    Google Scholar 

  • Song, J., Hwang, J., Kang, I. & Cho, J.-C. A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments. Sci. Rep. 11, 19978 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices. Proc. Biol. Sci. 286, 20182448 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Christian, N., Whitaker, B. K. & Clay, K. Microbiomes: Unifying animal and plant systems through the lens of community ecology theory. Front. Microbiol. 6, 869 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zieman, J. C. Productivity in seagrasses: Methods and rates. In Handbook of Seagrass Biology: An ecosystem perspective (eds Phillips, R. C. & McRoy, C. P.) 87–116 (Garland STPM Press, 1980).

    Google Scholar 

  • Dennison, W. C. Leaf production. Seagrass research methods, UNESCO, Paris 77–79 (1990).

  • Walters, W. et al. Improved bacterial 16S rRNA gene (V4 and V4–5) and fungal internal transcribed spacer marker gene primers for microbial community surveys. mSystems 1, e00009-15 (2016).

    Article 
    PubMed 

    Google Scholar 

  • Comeau, A. M., Douglas, G. M. & Langille, M. G. I. Microbiome Helper: A custom and streamlined workflow for microbiome research. mSystems 2, e00127-16 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Wright, E. S. DECIPHER: Harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinform. 16, 322 (2015).

    Article 

    Google Scholar 

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Britton, T., Anderson, C. L., Jacquet, D., Lundqvist, S. & Bremer, K. Estimating divergence times in large phylogenetic trees. Syst. Biol. 56, 741–752 (2007).

    Article 
    PubMed 

    Google Scholar 

  • McMurdie, P. J. & Holmes, S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Paradis, E. & Schliep, K. ape 50: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35, 526–528 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Silverman, J. D., Washburne, A. D., Mukherjee, S. & David, L. A. A phylogenetic transform enhances analysis of compositional microbiota data. Elife 6, 1–20 (2017).

    Article 

    Google Scholar 

  • McMurdie, P. J. & Holmes, S. Waste not, want not: Why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Webb, C. O., Ackerly, D. D. & Kembel, S. W. Phylocom: Software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24, 2098–2100 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Russel, J. Russel88/MicEco: v0.9.15. (2021). 10.5281/zenodo.4733747.

  • Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26, 1463–1464 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar 

  • Friedman, J., Hastie, T. & Tibshirani, R. Regularization paths for generalized linear models via coordinate descent. J. Stat. Softw. 33, 1–22 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kahle, D. & Wickham, H. Ggmap: Spatial visualization with ggplot2. R J. 5, 144 (2013).

    Article 

    Google Scholar 


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