Cargando…

Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates

Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhou, Fangyuan, Wu, Xiaoqing, Gao, Yunxiao, Fan, Susu, Zhou, Hongzi, Zhang, Xinjian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9159939/
https://www.ncbi.nlm.nih.gov/pubmed/35663868
http://dx.doi.org/10.3389/fmicb.2022.878409
_version_ 1784719167159533568
author Zhou, Fangyuan
Wu, Xiaoqing
Gao, Yunxiao
Fan, Susu
Zhou, Hongzi
Zhang, Xinjian
author_facet Zhou, Fangyuan
Wu, Xiaoqing
Gao, Yunxiao
Fan, Susu
Zhou, Hongzi
Zhang, Xinjian
author_sort Zhou, Fangyuan
collection PubMed
description Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2–3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora.
format Online
Article
Text
id pubmed-9159939
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-91599392022-06-03 Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates Zhou, Fangyuan Wu, Xiaoqing Gao, Yunxiao Fan, Susu Zhou, Hongzi Zhang, Xinjian Front Microbiol Microbiology Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2–3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora. Frontiers Media S.A. 2022-05-19 /pmc/articles/PMC9159939/ /pubmed/35663868 http://dx.doi.org/10.3389/fmicb.2022.878409 Text en Copyright © 2022 Zhou, Wu, Gao, Fan, Zhou and Zhang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Zhou, Fangyuan
Wu, Xiaoqing
Gao, Yunxiao
Fan, Susu
Zhou, Hongzi
Zhang, Xinjian
Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title_full Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title_fullStr Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title_full_unstemmed Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title_short Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates
title_sort diversity shifts in the root microbiome of cucumber under different plant cultivation substrates
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9159939/
https://www.ncbi.nlm.nih.gov/pubmed/35663868
http://dx.doi.org/10.3389/fmicb.2022.878409
work_keys_str_mv AT zhoufangyuan diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates
AT wuxiaoqing diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates
AT gaoyunxiao diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates
AT fansusu diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates
AT zhouhongzi diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates
AT zhangxinjian diversityshiftsintherootmicrobiomeofcucumberunderdifferentplantcultivationsubstrates