TY - JOUR
T1 - Metagenomic analysis of the bacterial community associated with the taproot of sugar beet
AU - Tsurumaru, Hirohito
AU - Okubo, Takashi
AU - Okazaki, Kazuyuki
AU - Hashimoto, Megumi
AU - Kakizaki, Kaori
AU - Hanzawa, Eiko
AU - Takahashi, Hiroyuki
AU - Asanome, Noriyuki
AU - Tanaka, Fukuyo
AU - Sekiyama, Yasuyo
AU - Ikeda, Seishi
AU - Minamisawa, Kiwamu
N1 - Publisher Copyright:
© 2015, Japanese Society of Microbial Ecology.All rights reserved.
PY - 2015
Y1 - 2015
N2 - We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N 2 fixation genes (nifHDK) were not detected; bacterial N2-fixing activity was not observed in the 15N2-feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N 2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.
AB - We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N 2 fixation genes (nifHDK) were not detected; bacterial N2-fixing activity was not observed in the 15N2-feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N 2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.
KW - Key words: bradyrhizobium
KW - Metagenome
KW - Plant growth-promoting bacteria
KW - Quinoprotein glucose dehydrogenase
KW - Sugar beet
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U2 - 10.1264/jsme2.ME14109
DO - 10.1264/jsme2.ME14109
M3 - Article
C2 - 25740621
AN - SCOPUS:84925450898
VL - 30
SP - 63
EP - 69
JO - Microbes and Environments
JF - Microbes and Environments
SN - 1342-6311
IS - 1
ER -