Cargando…
Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota
Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species compositio...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7022885/ https://www.ncbi.nlm.nih.gov/pubmed/31878183 http://dx.doi.org/10.3390/microorganisms8010038 |
_version_ | 1783498121044557824 |
---|---|
author | Chialva, Matteo Ghignone, Stefano Novero, Mara Hozzein, Wael N. Lanfranco, Luisa Bonfante, Paola |
author_facet | Chialva, Matteo Ghignone, Stefano Novero, Mara Hozzein, Wael N. Lanfranco, Luisa Bonfante, Paola |
author_sort | Chialva, Matteo |
collection | PubMed |
description | Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research. |
format | Online Article Text |
id | pubmed-7022885 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-70228852020-03-12 Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota Chialva, Matteo Ghignone, Stefano Novero, Mara Hozzein, Wael N. Lanfranco, Luisa Bonfante, Paola Microorganisms Article Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research. MDPI 2019-12-24 /pmc/articles/PMC7022885/ /pubmed/31878183 http://dx.doi.org/10.3390/microorganisms8010038 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Chialva, Matteo Ghignone, Stefano Novero, Mara Hozzein, Wael N. Lanfranco, Luisa Bonfante, Paola Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title | Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title_full | Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title_fullStr | Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title_full_unstemmed | Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title_short | Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota |
title_sort | tomato rna-seq data mining reveals the taxonomic and functional diversity of root-associated microbiota |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7022885/ https://www.ncbi.nlm.nih.gov/pubmed/31878183 http://dx.doi.org/10.3390/microorganisms8010038 |
work_keys_str_mv | AT chialvamatteo tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota AT ghignonestefano tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota AT noveromara tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota AT hozzeinwaeln tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota AT lanfrancoluisa tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota AT bonfantepaola tomatornaseqdataminingrevealsthetaxonomicandfunctionaldiversityofrootassociatedmicrobiota |