Phytobiomes are compositionally nested from the ground up

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1 Department of Botany, University of Hawaii at Manoa, Honolulu, Hawaii, United States
2 Department of Botany, University of Hawaii at Manoa, Honolulu, HI, United States
3 Department of Biology, University of Hawaii at Manoa, Honolulu, HI, United States
4 Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States
5 Marine Biology, University of Hawaii at Manoa, Honolulu, HI, United States
6 Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Honolulu, HI, United States
7 Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI, United States
8 Department of Natural Resources and Environmental Management, University of Hawaii at Manoa, Honolulu, HI, United States
9 Department Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States
DOI
10.7287/peerj.preprints.27393v1
Published
Accepted
Subject Areas
Ecology, Microbiology, Plant Science
Keywords
Phytobiomes, Nestedness, Isolation by Distance, 16S, Plant Microbiome
Copyright
© 2018 Amend et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Amend AS, Cobian GM, Laruson AJ, Remple K, Tucker SJ, Poff KE, Antaky C, Boraks A, Jones CA, Kuehu D, Lensing BR, Pejhanmehr M, Richardson DT, Riley PP. 2018. Phytobiomes are compositionally nested from the ground up. PeerJ Preprints 6:e27393v1

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.

Author Comment

This is a submission to PeerJ for review.

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.

DOI: 10.7287/peerj.preprints.27393v1/supp-1

Significant indicator species for plant parts

DOI: 10.7287/peerj.preprints.27393v1/supp-3

Mantel tests measure the correlation between geographic distance and microbial community dissimilarity for Scaevola taccada surface microbes, including all Kailua individuals

DOI: 10.7287/peerj.preprints.27393v1/supp-4