Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria.
A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 μmol.mol(-1)) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.
Environmental Biofunction Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan ; Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University Sendai, Japan.
Takashi
T
Okubo
Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya University Nagoya, Japan.
Dongyan
D
Liu
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University Sendai, Japan.
Hirohito
H
Tsurumaru
Large-scale Farming Research Division, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization Hokkaido, Japan.
Seishi
S
Ikeda
Division of Bioresource Functions, Graduate School of Bioagricultural Sciences, Nagoya University Nagoya, Japan.
Susumu
S
Asakawa
Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Takeshi
T
Tokida
Environmental Biofunction Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Kanako
K
Tago
Environmental Biofunction Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Masahito
M
Hayatsu
Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan.
Naohiro
N
Aoki
Division of Plant Sciences, National Institute of Agrobiological Sciences Tsukuba, Japan.
Ken
K
Ishimaru
Division of Plant Sciences, National Institute of Agrobiological Sciences Tsukuba, Japan.
Kazuhiro
K
Ujiie
Agro-Meteorology Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Yasuhiro
Y
Usui
Taiyo-Keiki Co., Ltd. Tokyo, Japan.
Hirofumi
H
Nakamura
Agro-Meteorology Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Hidemitsu
H
Sakai
Carbon and Nutrient Cycles Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Kentaro
K
Hayashi
Agro-Meteorology Division, National Institute for Agro-Environmental Sciences Tsukuba, Japan.
Toshihiro
T
Hasegawa
Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University Sendai, Japan.
Kiwamu
K
Minamisawa
16S rRNA gene; FACE; methane; rice; root