Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

Okubo, Takashi; Liu, Dongyan; Tsurumaru, Hirohito; Ikeda, Seishi; Asakawa, Susumu; Tokida, Takeshi; Tago, Kanako; Hayatsu, Masahito; Aoki, Naohiro; Ishimaru, Ken; Ujiie, Kazuhiro; Usui, Yasuhiro; Nakamura, Hirofumi; Sakai, Hidemitsu; Hayashi, Kentaro; Hasegawa, Toshihiro; Minamisawa, Kiwamu

doi:10.3389/fmicb.2015.00136

Cited by 43 publications

(23 citation statements)

References 39 publications

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“…A parallel study to the present study demonstrated that the abundance of methane-oxidizing bacteria in rice roots decreased under elevated [CO 2 ], which interacted with elevated soil temperature in the paddy field (31). The results of the present study demonstrated that a similar effect occurred in bulk soil.…”

Section: Discussionsupporting

confidence: 61%

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Chen

Tago

Hayatsu

et al. 2016

Microbes and environments

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Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

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Section: Discussionsupporting

confidence: 61%

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Chen

Tago

Hayatsu

et al. 2016

Microbes and environments

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“…Recent studies have revealed only minor changes in soil microbial communities under eCO 2 [8]. But it is important to understand microbial response to increasing (CO 2 ) to predict its effects on soil as plant-associated microbes produce plant hormones, fix nitrogen, and oxidize methane [9].…”

Section: Introductionmentioning

confidence: 99%

Impact of Elevated CO2 on Wheat Growth and Yield under Free Air CO2 Enrichment

Pandey¹,

Sharma²,

Deeba³

et al. 2017

AJCC

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Impact of elevated CO 2 (free air CO 2 enrichment) was studied on wheat (Triticum aestivum L. var Kundan) growth, yield and proteome. Elevated CO 2 significantly impacted both underground (+24%) and aboveground (+15%) biomass. Grain weight/plant and harvest index were increased by 35% and 11.4%, respectively under high CO 2 . On the other hand, seed protein content was decreased by 19% under CO 2 enrichment while seed starch and soluble sugar contents were increased by 8% and 23%, respectively. Wheat leaf proteomics revealed that 50 proteins were showing differential expression. Twenty proteins were more abundant while 30 were less abundant. Thirty two proteins were identified by MALDI TOF TOF. More abundant proteins were related to defense, photosynthesis, energy metabolism etc. While less abundant proteins were related to glycolysis and gluconeogenesis. Wheat grain proteomics revealed that out of 49 differentially abundant proteins, 24 were more in abundance and 25 were less in abundance in wheat grains under eCO 2 condition. Thirty three proteins were identified and functionally characterized. They were found to be involved mainly in carbon metabolism, storage, defence and proteolysis. Gluten proteins are the major component of wheat storage proteins. Our results showed that both high and low molecular weight glutenins were more in eCO 2 wheat seeds while there was no change in gliadin evels. This might alter wheat dough strength. Concentration of grain Cr and As was increased at eCO 2 while that of Fe, Cu, Zn and Se were found to be decreased. Dynamics of carbon utilization and metabolic abilities of soil microbes under eCO 2 were significantly altered. Our study showed that altered wheat seed composition is cause for concern vis-à-vis nutrition and health and for industries which may have implications for agriculturally dominated country like India.

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“…Das and Adhya (2012) noted that an increase of methanogenic population with elevated CO 2 levels was the most important reason for enhanced CH 4 production under CO 2 enrichment. In a free air CO 2 enrichment (FACE) experiment, Okubo et al (2015) also found that the number of copies of the mcrA gene significantly increased when CO 2 concentrations were elevated in rice paddy fields. Similarly, our results showed that elevated CO 2 concentrations significantly increased the abundance of methanogens in the rice rhizosphere soil ( Figure 1 ).…”

Section: Discussionmentioning

confidence: 94%

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field

Liu

Cheng

et al. 2016

Front. Microbiol.

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Although climate change is predicted to affect methane (CH4) emissions in paddy soil, the dynamics of methanogens and methanotrophs in paddy fields under climate change have not yet been fully investigated. To address this issue, a multifactor climate change experiment was conducted in a Chinese paddy field using the following experimental treatments: (1) enrichment of atmospheric CO2 concentrations (500 ppm, CE), (2) canopy air warming (2°C above the ambient, WA), (3) combined CO2 enrichment and warming (CW), and (4) ambient conditions (CK). We analyzed the abundance of methanogens and methanotrophs, community structures, CH4 production and oxidation potentials, in situ CH4 emissions using real-time PCR, T-RFLP, and clone library techniques, as well as biochemical assays. Compared to the control under CE and CW treatments, CH4 production potential, methanogenic gene abundance and soil microbial biomass carbon significantly increased; the methanogenic community, however, remained stable. The canopy air warming treatment only had an effect on CH4 oxidation potential at the ripening stage. Phylogenic analysis indicated that methanogens in the rhizosphere were dominated by Methanosarcina, Methanocellales, Methanobacteriales, and Methanomicrobiales, while methanotrophic sequences were classified as Methylococcus, Methylocaldum, Methylomonas, Methylosarcina (Type I) and Methylocystis (Type II). However, the relative abundance of Methylococcus (Type I) decreased under CE and CW treatments and the relative abundance of Methylocystis (Type II) increased. The in situ CH4 fluxes indicated similar seasonal patterns between treatments; both CE and CW increased CH4 emissions. In conclusion results suggest that methanogens and methanotrophs respond differently to elevated atmospheric CO2 concentrations and warming, thus adding insights into the effects of simulated global climate change on CH4 emissions in paddy fields.

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Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

Cited by 43 publications

References 39 publications

Effect of Elevated CO<sub>2</sub> Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Effect of Elevated CO<sub>2</sub> Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Impact of Elevated CO<sub>2</sub> on Wheat Growth and Yield under Free Air CO<sub>2</sub> Enrichment

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field

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Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria

Cited by 43 publications

References 39 publications

Effect of Elevated CO<sub>2</sub> Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Effect of Elevated CO<sub>2</sub> Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil

Impact of Elevated CO&lt;sub&gt;2&lt;/sub&gt; on Wheat Growth and Yield under Free Air CO&lt;sub&gt;2&lt;/sub&gt; Enrichment

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field

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Impact of Elevated CO<sub>2</sub> on Wheat Growth and Yield under Free Air CO<sub>2</sub> Enrichment