Globalscale structure of the eelgrass microbiome

Ashkaan K. Fahimipour, Melissa R. Kardish, Jenna M. Lang, Jessica L. Green, Jonathan A Eisen, John J. Stachowicz

Research output: Contribution to journalArticlepeer-review

68 Scopus citations


Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here, we report the results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition, and variability of microbial communities associated with eelgrass. We also investigated hypotheses about the assembly of the eelgrass microbiome using a metabolic modeling approach. Our results reveal leaf communities displaying high variability and spatial turnover that mirror their adjacent coastal seawater microbiomes. By contrast, roots showed relatively low compositional turnover and were distinct from surrounding sediment communities, a result driven by the enrichment of predicted sulfur-oxidizing bacterial taxa on root surfaces. Predictions from metabolic modeling of enriched taxa were consistent with a habitat-filtering community assembly mechanism whereby similarity in resource use drives taxonomic cooccurrence patterns on belowground, but not aboveground, host tissues. Our work provides evidence for a core eelgrass root microbiome with putative functional roles and highlights potentially disparate processes influencing microbial community assembly on different plant compartments.

Original languageEnglish (US)
Article numbere03391-16
JournalApplied and Environmental Microbiology
Issue number12
StatePublished - Jun 1 2017


  • Phyllosphere-inhabiting microbes
  • Plant-microbe interactions
  • Rhizosphere-inhabiting microbes
  • Seagrass

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology


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