Nitrate supply-dependent shifts in communities of root-associated bacteria in Arabidopsis

Noriyuki Konishi, Takashi Okubo, Tomoyuki Yamaya, Toshihiko Hayakawa, Kiwamu Minamisawa

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.

Original languageEnglish
Pages (from-to)314-323
Number of pages10
JournalMicrobes and Environments
Volume32
Issue number4
DOIs
Publication statusPublished - Jan 1 2017
Externally publishedYes

Fingerprint

nitrates
Arabidopsis
nitrate
bacterium
bacteria
bacterial communities
Burkholderiaceae
relative abundance
Rhizobiaceae
ribosomal RNA
plant growth
Bradyrhizobiaceae
soil bacteria
intergenic DNA
RNA
transcription factors
DNA
ecosystems
gene
ecosystem

Keywords

  • Arabidopsis
  • NIN-like protein
  • Nitrate
  • Root-associated bacterial communities
  • TCP20

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Soil Science
  • Plant Science

Cite this

Nitrate supply-dependent shifts in communities of root-associated bacteria in Arabidopsis. / Konishi, Noriyuki; Okubo, Takashi; Yamaya, Tomoyuki; Hayakawa, Toshihiko; Minamisawa, Kiwamu.

In: Microbes and Environments, Vol. 32, No. 4, 01.01.2017, p. 314-323.

Research output: Contribution to journalArticle

Konishi, Noriyuki ; Okubo, Takashi ; Yamaya, Tomoyuki ; Hayakawa, Toshihiko ; Minamisawa, Kiwamu. / Nitrate supply-dependent shifts in communities of root-associated bacteria in Arabidopsis. In: Microbes and Environments. 2017 ; Vol. 32, No. 4. pp. 314-323.
@article{8bdf4952382d4b8b96dd14303b13325d,
title = "Nitrate supply-dependent shifts in communities of root-associated bacteria in Arabidopsis",
abstract = "Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8{\%} was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.",
keywords = "Arabidopsis, NIN-like protein, Nitrate, Root-associated bacterial communities, TCP20",
author = "Noriyuki Konishi and Takashi Okubo and Tomoyuki Yamaya and Toshihiko Hayakawa and Kiwamu Minamisawa",
year = "2017",
month = "1",
day = "1",
doi = "10.1264/jsme2.ME17031",
language = "English",
volume = "32",
pages = "314--323",
journal = "Microbes and Environments",
issn = "1342-6311",
publisher = "Japanese Society Of Microbial Ecology",
number = "4",

}

TY - JOUR

T1 - Nitrate supply-dependent shifts in communities of root-associated bacteria in Arabidopsis

AU - Konishi, Noriyuki

AU - Okubo, Takashi

AU - Yamaya, Tomoyuki

AU - Hayakawa, Toshihiko

AU - Minamisawa, Kiwamu

PY - 2017/1/1

Y1 - 2017/1/1

N2 - Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.

AB - Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.

KW - Arabidopsis

KW - NIN-like protein

KW - Nitrate

KW - Root-associated bacterial communities

KW - TCP20

UR - http://www.scopus.com/inward/record.url?scp=85040130042&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040130042&partnerID=8YFLogxK

U2 - 10.1264/jsme2.ME17031

DO - 10.1264/jsme2.ME17031

M3 - Article

VL - 32

SP - 314

EP - 323

JO - Microbes and Environments

JF - Microbes and Environments

SN - 1342-6311

IS - 4

ER -