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

NosZ I carrying microorganisms determine N2O emissions from the subtropical paddy field under elevated CO2 and strongly CO2-responsive cultivar

Elevated CO2 (eCO2) decreases N2O emissions from subtropical paddy fields, but the underlying mechanisms remain to be investigated. Herein, the response of key microbial nitrogen cycling genes to eCO2 (ambient air +200 μmol CO2 mol-1) in four rice cultivars, including two weakly CO2-responsive (W27, H5) and two strongly CO2-responsive cultivars (Y1540, L1988), was investigated. Except for nosZ I, eCO2 did not significantly alter the abundance of the other genes. NosZ I was a crucial factor governing N2O emissions, especially under eCO2 and a strongly responsive cultivar. eCO2 affected the nosZ I gene abundance (p < 0.05), for instance, the nosZ I gene abundance of cultivar W27 increased from 1.53 × 107 to 2.86 × 107 copies g-1 dw soil (p < 0.05). In the nosZ I microbial community, the known taxa were mainly Pseudomonadota (phylum) (19.74-31.72 %) and Alphaproteobacteria (class) (0.56-13.12 %). In the nosZ I community assembly process, eCO2 enhanced the role of stochasticity, increasing from 35 % to 85 % (p < 0.05), thereby inducing diffusion limitations of weakly responsive cultivars to dominate (67 %). Taken together, the increase in nosZ I gene abundance is a potential reason for the alleviation of N2O emissions from subtropical paddy fields under eCO2.

Does elevated CO2 enhance the arsenic uptake by rice? Yes or maybe: Evidences from FACE experiments

Elevated CO₂ (eCO₂) strongly affects rice yield and quality in arsenic (As) paddy soils. However, understanding of the As accumulation in rice under coupled stress of eCO₂ and soil As is still limited while data are scarce. It greatly limits the prediction for future rice safety. This study investigated the As uptake by rice grown in different As paddy soils under two CO₂ conditions (ambient and ambient +200 μmol mol^-1) in the free-air CO₂ enrichment (FACE) system. Results showed that eCO₂ lowered soil Eh at the tillering stage and caused higher concentrations of dissolved As and Fe²⁺ in soil pore water. Compared with the control, the increased As transfer abilities in rice straws under eCO₂ contributed to the higher As accumulation in rice grains, and their total As concentrations were increased by 10.3-31.2%. Besides, the increased amounts of iron plaque (IP) under eCO₂ failed to effectively inhibit the As uptake by rice due to the difference in critical stage between As immobilized by IP (mainly in maturing stage) and uptake by rice roots (about 50% contribution before filling stage). Risk assessments suggest that eCO₂ enhanced the human health risks of As intake from rice grains produced in low-As paddy soils (<30 mg kg^-1). In order to alleviate the As threats to rice under eCO₂, we consider that proper soil drainage before filling stage to improve soil Eh can serve as an effective way to reduce As uptake by rice. Pursuing appropriate rice varieties to reduce the As transfer ability may be the other positive strategy.

Effects of abrupt and gradual increase of atmospheric CO2 concentration on methanotrophs in paddy fields

The simulation of abrupt atmospheric CO₂ increase is a common way to examine the response of soil methanotrophs to future climate change. However, atmosphere is undergoing a gradual CO₂ increase, and it is unknown whether the previously reported response of methanotrophs to abrupt CO₂ increase can well represent their response to the gradual increase. To improve the understanding of the effect of elevated CO₂ (eCO₂) on methanotrophs in paddy ecosystems, the methane oxidation potential and communities of methanotrophs were examined via open top chambers under the three following CO₂ treatments: an ambient CO₂ concentration (AC); an abrupt CO₂ increase by 200 ppm above AC (AI); a gradual CO₂ increase by 40 ppm each year until 200 ppm above AC (GI). Relative to AC treatment, AI and GI treatments significantly (p < 0.05) increased the methane oxidation rate by 43.8% and 36.7%, respectively, during rice growth period. Furthermore, the abundance of pmoA genes was significantly (p < 0.05) increased by 62.4% and 32.5%, respectively, under AI and GI treatments. However, there were no significant variations in oxidation rate or gene abundance between the two eCO₂ treatments. In addition, no obvious change of overall community composition of methanotrophs was observed among treatments, while the proportions of Methylosarcina and Methylocystis significantly (p < 0.05) changed. Taken together, our results indicate similar response of methanotrophs to abrupt and gradual CO₂ increase, although the magnitude of response under gradual increase was smaller and the abrupt increase may somewhat overestimate the response.

Effects of elevated CO2 on the Cd uptake by rice in Cd-contaminated paddy soils

The rising atmospheric CO₂ is a major driver for climate change, directly affects rice production. Cadmium (Cd) in paddy soils also serves as a persistent concern. Currently, few studies consider the rice response to coupled stresses of elevated CO₂ (eCO₂) and soil Cd. Experimental evidence understanding the effects and mechanisms of eCO₂ on Cd uptake by rice is lacking yet. In a free-air CO₂ enrichment (FACE) system, a 3-year pot experiment was conducted to explore the Cd uptake by rice under two CO₂ conditions (ambient and ambient + 200 µmol·mol^-1) using combinations of in-situ Cd-contaminated soils and associated rice varieties. Results showed that more low-crystalline Fe oxides (Feh) in iron plaque (IP) were deposited on root surface with the increased dissolved Fe²⁺ due to lower soil redox status under eCO₂. The Cd accumulation in rice was hindered due to more Cd associated with Feh (Feh-Cd) rather than uptake by roots. Taken together, the relative effects of eCO₂ on Cd uptake by rice were consistent across years under different Cd-contaminated soils. Our findings will help to better understand the Cd uptake by rice under future climate conditions, and thus push the development of climate-crop-soil models and accurate prediction for food security.

Does wood mulch trigger microbially mediated positive plant-soil feedback in degraded boreal forest sites? A post hoc study

Introduction

Reforestation of degraded lands in the boreal forest is challenging and depends on the direction and strength of the plant-soil feedback (PSF).

Methods

Using a gradient in tree productivity (null, low and high) from a long-term, spatially replicated reforestation experiment of borrow pits in the boreal forest, we investigated the interplay between microbial communities and soil and tree nutrient stocks and concentrations in relation to a positive PSF induced by wood mulch amendment.

Results

Three levels of mulch amendment underlie the observed gradient in tree productivity, and plots that had been amended with a continuous layer of mulch 17 years earlier showed a positive PSF with trees up to 6 m tall, a closed canopy, and a developing humus layer. The average taxonomic and functional composition of the bacterial and fungal communities differed markedly betweenlow- and high-productivity plots. Trees in high-productivity plots recruited a specialized soil microbiome that was more efficient at nutrient mobilization and acquisition. These plots showed increases in carbon (C), calcium (Ca), nitrogen (N), potassium (K), and phosphorus (P) stocks and as well as bacterial and fungal biomass. The soil microbiome was dominated by taxa from the fungal genus Cortinarius and the bacterial family Chitinophagaceae, and a complex microbial network with higher connectivity and more keystone species supported tree productivity in reforested plots compared to unproductive plots.

Discussion

Therefore, mulching of plots resulted in a microbially mediated PSF that enhances mineral weathering and non-symbiotic N fixation, and in turn helps transform unproductive plots into productive plots to ensure rapid restoration of the forest ecosystem in a harsh boreal environment.

Effects of elevated CO2 and warming on the root-associated microbiota in an agricultural ecosystem

Plant root-associated microbial communities profoundly affect plant nutrition and productivity. Although elevated atmospheric CO₂ and warming affect above- and belowground plant processes, it remains unclear how root-associated microbial communities respond to elevated CO₂ and warming. In this study, an open-air field experiment was conducted to assay the interactive effects of elevated CO₂ (500 ppm) and warming (+2°C) on the root-associated microbiota and soil enzyme activities in a rice-wheat rotation ecosystem. The results revealed that elevated CO₂ significantly increased rhizosphere soil organic carbon (SOC) and total nitrogen contents. In addition, glucosidase, β-xylosidase, and phosphatase activities significantly increased. The richness and Shannon diversity indices were significantly higher in rhizosphere soil than in root endosphere. Elevated CO₂ and warming significantly impacted the rhizosphere soil microbiota and altered their composition by changing the relative abundance of some specific groups. Soil pH, SOC, and available potassium content significantly altered the dominant bacterial phyla in the rhizosphere. SOC affected root endophytic bacterial phyla. Bacterial and fungal genera were significantly correlated with soil variables in the rhizosphere than in the root endosphere. These results indicate that microbial communities in the rhizosphere are more sensitive to elevated CO₂ and warming than those in the root endosphere.

Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo), catalyzed by bacteria closely related to Candidatus Methylomirabilis oxyfera, links the global carbon and nitrogen cycles. Currently, the contribution of n-damo in controlling methane emissions and nitrogen removal, and the key regulatory factors of this process in Chinese paddy fields are poorly known. Here, soil samples from 20 paddy fields located in different climate zones across China were collected to examine the n-damo activity and bacterial communities. The n-damo activity and bacterial abundance varied from 1.05 to 5.97 nmol CH₄ g^-1 (dry soil) d^-1 and 2.59 × 10⁵ to 2.50 × 10⁷ copies g^-1 dry soil, respectively. Based on the n-damo activity, it was estimated that approximately 0.91 Tg CH₄ and 2.17 Tg N could be consumed annually via n-damo in Chinese paddy soils. The spatial variations in n-damo activity and community structure of n-damo bacteria were significantly (p < 0.05) affected by the soil ammonium content, labile organic carbon content and pH. Furthermore, significant differences in n-damo activity, bacterial abundance and community composition were observed among different climate zones. The n-damo activity was found to be positively correlated with the mean annual air temperature. Taken together, our results demonstrated the potential importance of n-damo in both methane consumption and nitrogen removal in Chinese paddy soils, and this process was regulated by local soil and climatic factors.

Elevated CO2 does not necessarily enhance greenhouse gas emissions from rice paddies

Elevated atmospheric carbon dioxide (eCO₂) greatly impacts greenhouse gas (GHG) emissions of CH₄ and N₂O from rice fields. Although eCO₂ generally stimulates GHG emissions in the short term (<5 years) experiments, the responses to long-term (≥10 years) eCO₂ remain poorly known. Here we show, through a series of experiments and meta-analysis, that the eCO₂ does not necessarily increase CH₄ and N₂O emissions from rice paddies. In an experiment of free-air CO₂ enrichment for 13-15 years, CH₄ and N₂O emissions were decreased by 11-54% and 33-54%, respectively. The decline of CH₄ emissions was related to the reduction of CH₄ production and enhancement of CH₄ oxidation via raising soil Eh and soil-water interface [O₂] under eCO₂. Moreover, the eCO₂ significantly decreased NH₄⁺-N content, suggesting a reduction of soil nitrification and thereby N₂O emissions. A meta-analysis showed that CH₄ and N₂O emissions were stimulated under short-term eCO₂ while reduced under long-term eCO₂. The eCO₂-induced increase in yield and biomass and the ratio of mcrA genes/pmoA genes declined with eCO₂ duration, indicating an eCO₂-stimulation of methanogenesis lower than that of methanotrophy over time by fewer increased substrates. Upscaling the results of meta-analysis, the eCO₂-induced global paddy CH₄ and N₂O emissions shifted from an increase (+0.17 Pg CO₂-eq year^-1) in the short term into a decrease (-0.11 Pg CO₂-eq year^-1) in the long term. Our findings suggest that the effect of eCO₂ on GHG emissions changes over time, and this should be considered in future climate change research.

Response of nitrite-dependent anaerobic methanotrophs to elevated atmospheric CO2 concentration in paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo) catalyzed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a new pathway for the regulation of methane emissions from paddy fields. Elevated atmospheric CO₂ concentrations (e[CO₂]) can indirectly affect the structure and function of microbial communities. However, the response of M. oxyfera-like bacteria to e[CO₂] is currently unknown. Here, we investigated the effect of e[CO₂] (ambient CO₂ + 200 ppm) on community composition, abundance, and activity of M. oxyfera-like bacteria at different depths (0-5, 5-10, and 10-20 cm) in paddy fields across multiple rice growth stages (tillering, jointing, and flowering). High-throughput sequencing showed that e[CO₂] had no significant effect on the community composition of M. oxyfera-like bacteria. However, quantitative PCR suggested that the 16S rRNA gene abundance of M. oxyfera-like bacteria increased significantly in soil under e[CO₂], particularly at the tillering stage. Furthermore, ¹³CH₄ tracer experiments showed potential n-damo activity of 0.31-8.91 nmol CO₂ g^-1 (dry soil) d^-1. E[CO₂] significantly stimulated n-damo activity, especially at the jointing and flowering stages. The n-damo activity and abundance of M. oxyfera-like bacteria increased by an average of 90.9% and 50.0%, respectively, under e[CO₂]. Correlation analysis showed that the increase in soil dissolved organic carbon content caused by e[CO₂] had significant effects on the activity and abundance of M. oxyfera-like bacteria. Overall, this study provides the first evidence for a positive response of M. oxyfera-like bacteria to e[CO₂], which may help reduce methane emissions from paddy fields under future climate change conditions.

Recent Developments in the Study of Plant Microbiomes

To date, an understanding of how plant growth-promoting bacteria facilitate plant growth has been primarily based on studies of individual bacteria interacting with plants under different conditions. More recently, it has become clear that specific soil microorganisms interact with one another in consortia with the collective being responsible for the positive effects on plant growth. Different plants attract different cross-sections of the bacteria and fungi in the soil, initially based on the composition of the unique root exudates from each plant. Thus, plants mostly attract those microorganisms that are beneficial to plants and exclude those that are potentially pathogenic. Beneficial bacterial consortia not only help to promote plant growth, these consortia also protect plants from a wide range of direct and indirect environmental stresses. Moreover, it is currently possible to engineer plant seeds to contain desired bacterial strains and thereby benefit the next generation of plants. In this way, it may no longer be necessary to deliver beneficial microbiota to each individual growing plant. As we develop a better understanding of beneficial bacterial microbiomes, it may become possible to develop synthetic microbiomes where compatible bacteria work together to facilitate plant growth under a wide range of natural conditions.

The process of methanogenesis in paddy fields under different elevated CO2 concentrations

Understanding the process of methanogenesis in paddy fields under the scenarios of future climate change is of great significance for reducing greenhouse gas emissions and regulating the soil carbon cycle. Methyl Coenzyme M Reductase subunit A (mcrA) of methanogens is a rate-limiting enzyme that catalyzes the final step of CH₄ production. However, the mechanism of methanogenesis change in the paddy fields under different elevated CO₂ concentrations (e[CO₂]) is rarely explored in earlier studies. In this research, we explored how the methanogens affect CH₄ flux in paddy fields under various (e[CO₂]). CH₄ flux and CH₄ production potential (MPP), and mcrA gene abundance were quantitatively analyzed under C (ambient CO₂ concentration), C₁ (C + 160 ppm CO₂), and C₂ (C + 200 ppm CO₂) treatments. Additionally, the community composition and structure of methanogens were also compared with Illumina MiSeq sequencing. The results showed that C₂ treatment significantly increased CH₄ flux and MPP at the tillering stage. E[CO₂] had a positive effect on the abundance of methanogens, but the effect was insignificant. We detected four known dominant orders of methanogenesis in this study, such as Methanosarcinales, Methanobacteriales, Methanocellales, and Methanomicrobiales. Although e[CO₂] did not significantly change the overall community structure and diversity of methanogens, C₂ treatment significantly reduced the relative abundance of two uncultured genera compared to C treatment. A linear regression model of DOC, methanogenic abundance, and MPP can explain 67.2% of the variation of CH₄ flux under e[CO₂]. Overall, our results demonstrated that CH₄ flux in paddy fields under e[CO₂] was mainly controlled by soil unstable C substrate and the abundance and activity of methanogens in rhizosphere soil.

Microbial functional genes commonly respond to elevated carbon dioxide

Atmospheric CO₂ concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO₂ enrichment (FACE) experimental sites have shown significant impacts of elevated CO₂ (eCO₂) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO₂ environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO₂, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO₂. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO₂ environment.

Effects of elevated carbon dioxide on environmental microbes and its mechanisms: A review

Before the industrial revolution, the atmospheric CO₂ concentration was 180-330 ppm; however, fossil-fuel combustion and forest destruction have led to increased atmospheric CO₂ concentration. CO₂ capture and storage is regarded as a promising strategy to prevent global warming and ocean acidification and to alleviate elevated atmospheric CO₂ concentration, but the leakage of CO₂ from storage system can lead to rapid acidification of the surrounding circumstance, which might cause negative influence on environmental microbes. The effects of elevated CO₂ on microbes have been reported extensively, but the review regarding CO₂ affecting different environmental microorganisms has never been done previously. Also, the mechanisms of CO₂ affecting environmental microorganisms are usually contributed to the change of pH values, while the direct influences of CO₂ on microorganisms were often neglected. This paper aimed to provide a systematic review of elevated CO₂ affecting environmental microbes and its mechanisms. Firstly, the influences of elevated CO₂ and potential leakage of CO₂ from storage sites on community structures and diversity of different surrounding environmental microbes were assessed and compared. Secondly, the adverse impacts of CO₂ on microbial growth, cell morphology and membranes, bacterial spores, and microbial metabolism were introduced. Then, based on biochemical principles and knowledge of microbiology and molecular biology, the fundamental mechanisms of the influences of carbon dioxide on environmental microbes were discussed from the aspects of enzyme activity, electron generation and transfer, and key gene and protein expressions. Finally, key questions relevant to the environmental effect of CO₂ that need to be answered in the future were addressed.

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers

Numerous studies have shown that the continuous increase of atmosphere CO2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO2 (eCO2) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO2 at both soil depths, although the stimulation effect of eCO2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO2 increases.IMPORTANCE The concentration of atmospheric carbon dioxide (CO2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO2 (eCO2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.

Soil Conditions Rather Than Long-Term Exposure to Elevated CO2 Affect Soil Microbial Communities Associated with N-Cycling

Continuously rising atmospheric CO₂ concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO₂ (eCO₂) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N₂O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO₂ (aCO₂). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO₂ effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO₂ on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO₂ and aCO₂, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO₂ differed only slightly from soil under aCO₂. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO₂ level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO₂ had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N₂O emissions under eCO₂ and future studies should aim at exploring the active members of the soil microbial community.

Methanogenic Community Was Stable in Two Contrasting Freshwater Marshes Exposed to Elevated Atmospheric CO2

The effects of elevated atmospheric CO₂ concentration on soil microbial communities have been previously recorded. However, limited information is available regarding the response of methanogenic communities to elevated CO₂ in freshwater marshes. Using high-throughput sequencing and real-time quantitative PCR, we compared the abundance and community structure of methanogens in different compartments (bulk soil, rhizosphere soil, and roots) of Calamagrostis angustifolia and Carex lasiocarpa growing marshes under ambient (380 ppm) and elevated CO₂ (700 ppm) atmospheres. C. lasiocarpa rhizosphere was a hotspot for potential methane production, based on the 10-fold higher abundance of the mcrA genes per dry weight. The two marshes and their compartments were occupied by different methanogenic communities. In the C. lasiocarpa marsh, archaeal family Methanobacteriaceae, Rice Cluster II, and Methanosaetaceae co-dominated in the bulk soil, while Methanobacteriaceae was the exclusively dominant methanogen in the rhizosphere soil and roots. Families Methanosarcinaceae and Methanocellaceae dominated in the bulk soil of C. angustifolia marsh. Conversely, Methanosarcinaceae and Methanocellaceae together with Methanobacteriaceae dominated in the rhizosphere soil and roots, respectively, in the C. angustifolia marsh. Elevated atmospheric CO₂ increased plant photosynthesis and belowground biomass of C. lasiocarpa and C. angustifolia marshes. However, it did not significantly change the abundance (based on mcrA qPCR), diversity, or community structure (based on high-throughput sequencing) of methanogens in any of the compartments, irrespective of plant type. Our findings suggest that the population and species of the dominant methanogens had weak responses to elevated atmospheric CO₂. However, minor changes in specific methanogenic taxa occurred under elevated atmospheric CO₂. Despite minor changes, methanogenic communities in different compartments of two contrasting freshwater marshes were rather stable under elevated atmospheric CO₂.

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers

The effect of elevated atmospheric CO₂ concentration [CO₂] on the diversity and composition of the prokaryotic community inhabiting the rhizosphere of winter barley (Hordeum vulgare L.) was investigated in a field experiment, using open‐top chambers. Rhizosphere samples were collected at anthesis (flowering stage) from six chambers with ambient [CO₂] (approximately 400 ppm) and six chambers with elevated [CO₂] (700 ppm). The V4 region of the 16S rRNA gene was PCR‐amplified from the extracted DNA and sequenced on an Illumina MiSeq instrument. Above‐ground plant biomass was not affected by elevated [CO₂] at anthesis, but plants exposed to elevated [CO₂] had significantly higher grain yield. The composition of the rhizosphere prokaryotic communities was very similar under ambient and elevated [CO₂]. The dominant taxa were Bacteroidetes, Actinobacteria, Alpha‐, Gamma‐, and Betaproteobacteria. Elevated [CO₂] resulted in lower prokaryotic diversity in the rhizosphere, but did not cause a significant difference in community structure.

Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors

Methane is one of the critical greenhouse gases, which absorb long wavelength radiation, affects the chemistry of atmosphere and contributes to global climate change. Rice ecosystem is one of the major anthropogenic sources of methane. The anaerobic waterlogged soil in rice field provides an ideal environment to methanogens for methanogenesis. However, the rate of methanogenesis differs according to rice cultivation regions due to a number of biological, environmental and physical factors like carbon sources, pH, Eh, temperature etc. The interplay between the different conditions and factors may also convert the rice fields into sink from source temporarily. Mechanistic understanding and comprehensive evaluation of these variations and responsible factors are urgently required for designing new mitigation options and evaluation of reported option in different climatic conditions. The objective of this review paper is to develop conclusive understanding on the methane production, oxidation, and emission and methane measurement techniques from rice field along with its mitigation/abatement mechanism to explore the possible reduction techniques from rice ecosystem.

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

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.

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

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.

Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root?

The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH₄–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N₂ fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of ¹⁵N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH₄ oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH₄-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH₄ oxidation and N₂ fixation).

Community Analysis of Root- and Tuber-Associated Bacteria in Field-Grown Potato Plants Harboring Different Resistance Levels against Common Scab

Eight genotypes of potato plants with different resistance levels against common scab were grown in a field infested with Streptomyces turgidiscabies. DNA was extracted from the roots, tubers, and rhizosphere soils of each of the eight genotypes at the flowering stage, and the quantity of S. turgidiscabies genomic DNA was assessed by real-time PCR using a TaqMan probe. The results obtained showed that the different potato genotypes had significant impacts on the population levels of S. turgidiscabies between resistant and susceptible genotypes in the tubers, but not in the roots or rhizosphere soils. Clone analyses of 16S rRNA gene libraries from the eight potato genotypes identified three phyla (Proteobacteria, Firmicutes, and Actinobacteria) as dominant taxa in root and tuber clone libraries, while a clustering analysis identified 391 operational taxonomic units (OTUs) at the species level. Eleven OTUs closely related to Aquicella siphonis, Arthrobacter nicotinovorans, Streptomyces rishiriensis, Rhodococcus baikonurensis, Rhizobium radiobacter, Rhizobium etli, Phyllobacterium myrsinacearum, Paenibacillus pabuli, Paenibacillus alginolyticus, and Bacillus halmapalus were detected in the root or tuber libraries of all the potato genotypes examined. Furthermore, an abundance of OTUs related to Aquicella and Rhodococcus was observed in the rhizospheres of resistant and susceptible potato genotypes, respectively. Based on this ecological information, an efficient survey may be conducted for biological agents from the potato rhizosphere.