4.7 Article

Effect of rice panicle size on paddy field CH4 emissions

期刊

BIOLOGY AND FERTILITY OF SOILS
卷 52, 期 3, 页码 389-399

出版社

SPRINGER
DOI: 10.1007/s00374-015-1084-2

关键词

Global warming; Food security; Greenhouse gas; Rice production; Spikelet number

资金

  1. National Key Technology Support Program of China [2011BAD16B14, 2015BAC02B02]
  2. Special Fund for Agro-scientific Research in the Public Interest [201503122]
  3. CAAS
  4. China Scholarship Council (CSC)
  5. Youth Science and Technology Innovation Foundation of Nanjing Agricultural University [KJ2012002]

向作者/读者索取更多资源

Developing large rice (Oryza sativa L.) panicles has been widely regarded as an effective approach to increasing rice yield. However, it is unclear whether panicle size affects CH4 emissions from rice fields, especially during the reproductive stage. Here, we conducted two experiments (rice variety and mutant) to examine the effects of rice panicle size on CH4 emissions. The variety experiment under field conditions at two sites showed that rice yield was significantly and positively correlated with the spikelet number. Mean CH4 emissions during the reproductive stage were significantly and negatively correlated with spikelet number. The rice mutant experiment under pot and field conditions using a wild-type rice variety (WT) and its mutant (Mutant) demonstrated that CH4 emissions were significantly lower in the former with large panicles than in the later with small panicles, during the reproductive and grain filling stages (P < 0.01), whereas the rice yields showed an opposite. Root exudates and soil dissolved organic C concentration were significantly lower under the WT than under the Mutant. Soil CH4 production potential and mcrA gene copy number of the soil under Mutant were significantly higher than those of the soil under WT. There was no significant difference in soil CH4 oxidation potential and pmoA gene copy number between soils of these two rice varieties. Our results suggest that developing large panicles would benefit rice production for high yield with low CH4 emission.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Environmental Sciences

Interactive effects of water management and liming on-CH4 emissions and rice cadmium uptake in an acid paddy soil

Yong Wang, Yanni Sun, Le Chen, Hua Shao, Yanhua Zeng, Yongjun Zeng, Feiyu Tang, Junhuo Cai, Shan Huang

Summary: Rice agriculture is a significant source of methane emissions and cadmium accumulation. The study investigated the combined effects of water management and lime application on CH4 emissions and rice Cd uptake. Results showed that flooding following midseason drainage effectively reduced CH4 emissions, while lime application reduced both CH4 emissions and rice Cd uptake. The recommended approach to mitigate CH4 emissions without increasing Cd uptake is continuous flooding with midseason drainage combined with lime application.

ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH (2023)

Article Biochemical Research Methods

Virus classification for viral genomic fragments using PhaGCN2

Jing-Zhe Jiang, Wen-Guang Yuan, Jiayu Shang, Ying-Hui Shi, Li-Ling Yang, Min Liu, Peng Zhu, Tao Jin, Yanni Sun, Li-Hong Yuan

Summary: The paper presents PhaGCN2, a tool that rapidly classifies viral sequences at the family level and improves the precision and recall of virus classification. It allows for high-throughput processing of viral sequences and supports visualization.

BRIEFINGS IN BIOINFORMATICS (2023)

Article Agronomy

Improving rice grain yield and reducing lodging risk simultaneously: A meta-analysis

Ping Liao, Stephen M. Bell, Le Chen, Shan Huang, Haiyuan Wang, Jiahui Miao, Yiming Qi, Yanni Sun, Bin Liao, Yongjun Zeng, Haiyan Wei, Hui Gao, Qigen Dai, Hongcheng Zhang

Summary: Smart agronomic management practices can reduce lodging risk in rice paddies. This includes employing lodging-resistant cultivars, appropriate fertilization, and applying plant growth regulators (PGRs). Additionally, the application of silicon, potassium, prohexadione calcium, and uniconazole can improve rice yield and reduce lodging risk.

EUROPEAN JOURNAL OF AGRONOMY (2023)

Article Multidisciplinary Sciences

Metabolic changes in bile acids with pregnancy progression and their correlation with perinatal complications in intrahepatic cholestasis of pregnant patients

Zhixin Ma, Yifeng Liu, Lin Chai, Guochen Jin, Yanni Sun, Shaomin Zhou, Peiyuan Yin, Siwen Wang, Yuning Zhu, Dan Zhang, Shiming Lu, Bo Zhu

Summary: Intrahepatic cholestasis of pregnancy (ICP) is a rare liver disease characterized by disordered bile acid metabolism during pregnancy. Different types of ICP show distinct bile acid metabolism profiles. Elevated levels of total bile acids and glycocholic acid are associated with preterm birth in early-onset ICP (EICP), while increased levels of total bile acids and taurocholic acid are predictive of preterm birth in late-onset ICP (LICP). This study highlights the importance of assessing bile acid metabolism in ICP patients to predict perinatal complications.

SCIENTIFIC REPORTS (2023)

Article Agriculture, Multidisciplinary

Interaction of lime application and straw retention on ammonia emissions from a double-cropped rice field

Ping Liao, Lei Liu, Stephen M. Bell, Jinsong Liu, Yanni Sun, Yongjun Zeng, Hongcheng Zhang, Shan Huang

Summary: Ammonia (NH3) emissions are a significant source of nitrogen (N) losses in rice paddies. Lime application and straw retention are commonly used practices to improve soil fertility in acidic soils. However, the interaction between lime and straw application on NH3 emissions from rice paddies is still unclear.

AGRICULTURE ECOSYSTEMS & ENVIRONMENT (2023)

Article Biochemical Research Methods

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer

Yongxin Ji, Jiayu Shang, Xubo Tang, Yanni Sun

Summary: Understanding the host range of plasmids is essential for studying their roles in bacterial evolution and adaptation. Existing tools for predicting plasmid hosts face challenges in sensitivity and precision. This study presents a hierarchical classification tool called HOTSPOT, which uses a state-of-the-art language model, Transformer, to accurately predict the host taxonomy of input plasmid contigs.

BIOINFORMATICS (2023)

Article Chemistry, Multidisciplinary

Laboratory Experiment and Application Evaluation of a Bio-Nano- depressurization and Injection-Increasing Composite System in Medium-Low Permeability Offshore Reservoirs

Qing Feng, Xianchao Chen, Ning Zhang, Xiaonan Li, Jingchao Zhou, Shengsheng Li, Xiaorong Zhang, Yanni Sun, Yuehui She

Summary: Bohai Oilfield has developed a bio-nano-depressurization and injection-increasing composite system solution to address the high injection pressure and insufficient injection volume in offshore oilfields. The new technology has the advantages of efficient decompression, long-term injection, and wide adaptation. However, there is a need for optimization schemes and application effect prediction methods to further promote and apply the bio-nano-composite system solution. This paper optimizes the injection volume, concentration, and speed of the bio-nano-augmentation fluid and evaluates the application effect using well testing, water absorption index, and numerical simulation methods.

ACS OMEGA (2023)

Article Biochemical Research Methods

PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer

Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun

Summary: In this study, a computational method called PhaVIP was developed for fast and accurate classification and annotation of phage virion proteins (PVPs). By encoding protein sequences into unique images and utilizing the Vision Transformer model, PhaVIP can learn both local and global features from sequence images. Experimental results demonstrated the superior performance of PhaVIP, and its output was further applied to phage taxonomy classification and phage host prediction with beneficial results.

BIOINFORMATICS (2023)

Article Biochemical Research Methods

HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses

Runzhou Yu, Syed Muhammad Umer Abdullah, Yanni Sun

Summary: Accessing accurate viral genomes is crucial for downstream data analysis. Although third-generation sequencing (TGS) is commonly used for virus sequencing due to its long read length, its higher per-base error rate poses a challenge. In this study, we developed HMMPolish, a novel pipeline for correcting errors in protein-coding regions of known RNA viruses. Using profile Hidden Markov Models, HMMPolish can correct errors that are ignored by other polishing tools. Extensive validation on different datasets demonstrated the superior performance of HMMPolish in error correction compared to popular polishers.

BRIEFINGS IN BIOINFORMATICS (2023)

Article Biochemistry & Molecular Biology

PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer

Xubo Tang, Jiayu Shang, Yongxin Ji, Yanni Sun

Summary: In this study, a plasmid detection tool called PLASMe was developed, which combines alignment and learning-based methods to effectively identify closely related and diverged plasmids. By encoding plasmid sequences as a language defined on the protein cluster-based token set, the Transformer model in PLASMe can learn the importance of proteins and their correlation. Comparative analysis showed that PLASMe achieved the highest F1-score in detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data, and exhibited more reliable performance than other tools.

NUCLEIC ACIDS RESEARCH (2023)

Article Multidisciplinary Sciences

LncRNA-Top: Controlled deep learning approaches for lncRNA gene regulatory relationship annotations across different platforms

Weidun Xie, Xingjian Chen, Zetian Zheng, Fuzhou Wang, Xiaowei Zhu, Qiuzhen Lin, Yanni Sun, Ka-Chun Wong

Summary: This study presents a method called lncRNA-Top to predict lncRNA-gene regulation relationships and constructs controlled deep-learning models. Through case studies, it is found that the predictions are accurate, and additional software is provided for target candidate annotation.

ISCIENCE (2023)

Article Biochemical Research Methods

PhaTYP: predicting the lifestyle for bacteriophages using BERT

Jiayu Shang, Xubo Tang, Yanni Sun

Summary: Researchers have developed a tool called PhaTYP that accurately predicts the lifestyle of bacteriophages, especially for short contigs. Experimental results show that PhaTYP outperforms other existing methods and achieves more stable performance on short contigs. Additionally, the utility of PhaTYP for analyzing phage lifestyle in human neonates' gut data has been demonstrated, which helps extend our understanding of microbial communities.

BRIEFINGS IN BIOINFORMATICS (2023)

Article Biochemical Research Methods

AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data

Runzhou Yu, Dehan Cai, Yanni Sun

Summary: RNA viruses mutate constantly, but accurate assembly of viral genomes is crucial for studying virus evolution and understanding the relationship between genotypes and virus properties. A new tool called AccuVIR has been developed for viral genome assembly and polishing using error-prone long reads. It can distinguish sequencing errors from true variants, resulting in more accurate viral genomes compared to other tools.

BIOINFORMATICS (2023)

Article Biochemical Research Methods

VirBot: an RNA viral contig detector for metagenomic data

Guowei Chen, Xubo Tang, Mang Shi, Yanni Sun

Summary: In this study, we developed VirBot, a simple yet effective RNA virus identification tool based on protein families and adaptive score cutoffs. Compared to seven popular tools for virus identification, VirBot demonstrated high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses on both simulated and real sequencing data.

BIOINFORMATICS (2023)

Article Soil Science

Liming reduces nitrogen uptake from chemical fertilizer but increases that from straw in a double rice cropping system

Ping Liao, Lei Liu, Jin Chen, Yanni Sun, Shan Huang, Yongjun Zeng, Kees Jan van Groenigen

Summary: Liming materials can increase rice yield and nitrogen uptake, but decrease the efficiency of fertilizer nitrogen and promote nitrogen losses. Long-term studies on the impact of liming on nitrogen dynamics in paddy soils are necessary.

SOIL & TILLAGE RESEARCH (2024)

暂无数据