Dataset Information

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

ABSTRACT:

Background

Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH₄) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks.

Results

The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH₄ emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH₄ emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~?30% determinism and ~?70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa.

Conclusions

These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.

SUBMITTER: Li D

PROVIDER: S-EPMC7825242 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

Li Dong D Ni Haowei H Jiao Shuo S Lu Yahai Y Zhou Jizhong J Sun Bo B Liang Yuting Y

Microbiome 20210122 1

<h4>Background</h4>Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH<sub>4</sub>) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interaction ...[more]

PMID: 33482926

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Project description:Background: Rice is understood to enhance methane emissions from paddy fields in IPCC guidelines. However, rice actually has two opposite functions related to methane: i) emission enhancement, such as by providing emission pathways (aerenchyma) and methanogenetic substrates; and ii) emission suppression by providing oxygen pathways, which suppress methanogenesis or enhance methane oxidation. The overall role of rice is thus determined by the balance between its enhancing and suppressing functions. Although previous studies have suggested that rice enhances total methane emissions, we aimed to demonstrate in high-emitting paddy fields that the overall methane emission is decreased by rice plants. Methods: We compared methane emissions with and without rice plants in triple cropping rice paddy fields in the Mekong Delta, Vietnam. The gas samples are collected using chamber method and ware analyzed by gas chromatography. Results: We found that rice, in fact, suppressed overall methane emissions in high-emitting paddies. The emission reductions increased with the growth of rice to the maximum tillering stage, then decreased after the heading stage, and finally recovered. Discussion: Our result indicates that the overall methane emission is larger than that of rice planted area. In addition, although many studies in standard-emitting paddies have found that the contribution of soil organic matter to methanogenesis is small, prior studies in high-emitting paddies suggest that methanogenesis depended mainly on soil organic matter accumulated from past crops. The higher the methane emission level, the lower the contribution of the rice-derived substrate; conversely, the higher the contribution of the rice providing oxygen. Finally, rice plants reduce methane emissions in high-emitting paddies. Conclusion: The present study demonstrates that during the growing season, rice is suppressing methane emissions in high-emitting paddies. This means the significance of using the rice variety which has high suppressing performance in high-emitting paddies.

Project description:Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.

Dataset Information

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

Background

Results

Conclusions

Publications

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

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