Phytobiomes are compositionally nested from the ground up
A peer-reviewed article of this Preprint also exists.
Author and article information
Abstract
Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning Oʻahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.
Cite this as
2018. Phytobiomes are compositionally nested from the ground up. PeerJ Preprints 6:e27393v1 https://doi.org/10.7287/peerj.preprints.27393v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a submission to PeerJ for review.
Sections
Supplemental Information
Box and whisker plots of dispersion of Jaccard beta diversity values within plant parts and soil samples
No dispersion means significantly differed in pairwise comparisons.
Mantel tests measure the correlation between geographic distance and microbial community dissimilarity for Scaevola taccada surface microbes, including all Kailua individuals
Additional Information
Competing Interests
Anthony S. Amend is an Academic Editor for PeerJ.
Author Contributions
Anthony S Amend conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Gerald M Cobian conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Aki J Laruson performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Kristina Remple performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Sarah J Tucker performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Kirsten E Poff performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Carmen Antaky performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Andre Boraks performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Casey A Jones performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Donna Kuehu performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Becca R Lensing performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Mersedeh Pejhanmehr performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Daniel T Richardson performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Paul P Riley performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Sequence data is deposited in the SRA as PRJNA385181.
Data Deposition
The following information was supplied regarding data availability:
Because this was a class project, code was generated by 12 students independently such that object names are not consistent. Collating these into a single readable format would be a massive undertaking. I regret not having organized this better at the onset and consider it an important lesson learned!
Funding
This work was supported by NSF grant #1255972 to Amend and NSF fellowship #1329626 to Cobian. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
