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Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841827/ https://www.ncbi.nlm.nih.gov/pubmed/29474469 http://dx.doi.org/10.1371/journal.pbio.2003862 |
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author | Edwards, Joseph A. Santos-Medellín, Christian M. Liechty, Zachary S. Nguyen, Bao Lurie, Eugene Eason, Shane Phillips, Gregory Sundaresan, Venkatesan |
author_facet | Edwards, Joseph A. Santos-Medellín, Christian M. Liechty, Zachary S. Nguyen, Bao Lurie, Eugene Eason, Shane Phillips, Gregory Sundaresan, Venkatesan |
author_sort | Edwards, Joseph A. |
collection | PubMed |
description | Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle. |
format | Online Article Text |
id | pubmed-5841827 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-58418272018-03-23 Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice Edwards, Joseph A. Santos-Medellín, Christian M. Liechty, Zachary S. Nguyen, Bao Lurie, Eugene Eason, Shane Phillips, Gregory Sundaresan, Venkatesan PLoS Biol Research Article Bacterial communities associated with roots impact the health and nutrition of the host plant. The dynamics of these microbial assemblies over the plant life cycle are, however, not well understood. Here, we use dense temporal sampling of 1,510 samples from root spatial compartments to characterize the bacterial and archaeal components of the root-associated microbiota of field grown rice (Oryza sativa) over the course of 3 consecutive growing seasons, as well as 2 sites in diverse geographic regions. The root microbiota was found to be highly dynamic during the vegetative phase of plant growth and then stabilized compositionally for the remainder of the life cycle. Bacterial and archaeal taxa conserved between field sites were defined as predictive features of rice plant age by modeling using a random forest approach. The age-prediction models revealed that drought-stressed plants have developmentally immature microbiota compared to unstressed plants. Further, by using genotypes with varying developmental rates, we show that shifts in the microbiome are correlated with rates of developmental transitions rather than age alone, such that different microbiota compositions reflect juvenile and adult life stages. These results suggest a model for successional dynamics of the root-associated microbiota over the plant life cycle. Public Library of Science 2018-02-23 /pmc/articles/PMC5841827/ /pubmed/29474469 http://dx.doi.org/10.1371/journal.pbio.2003862 Text en © 2018 Edwards et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Edwards, Joseph A. Santos-Medellín, Christian M. Liechty, Zachary S. Nguyen, Bao Lurie, Eugene Eason, Shane Phillips, Gregory Sundaresan, Venkatesan Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title | Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title_full | Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title_fullStr | Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title_full_unstemmed | Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title_short | Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
title_sort | compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841827/ https://www.ncbi.nlm.nih.gov/pubmed/29474469 http://dx.doi.org/10.1371/journal.pbio.2003862 |
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