Article
Agriculture, Multidisciplinary
Robert Crystal-Ornelas, Resham Thapa, Katherine L. Tully
Summary: This meta-analysis investigates the effects of BMPs on soil health within organic farming systems, showing significant improvements in SOC and MBC concentrations. Organic amendments and conservation tillage practices have positive impacts on soil health, while cover cropping can increase SOC concentrations significantly after 5 years.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Soil Science
Peng Li, Yuanbin Li, Luyao Xu, Huijuan Zhang, Xueshan Shen, Haofan Xu, Jiaguo Jiao, Huixin Li, Feng Hu
Summary: Proper recycling of agricultural waste is crucial for soil productivity and environmental health, and the use of organic amendments can significantly increase crop yield and soil quality index. However, further research is needed on the combined use of organic amendments and other farmland management practices to promote sustainable development in agriculture.
Article
Agriculture, Multidisciplinary
Rachel Wooliver, Sindhu Jagadamma
Summary: Agroecosystems have a large potential for soil carbon sequestration, and cover cropping is an effective management practice that can enhance soil carbon while providing other ecological and agronomic benefits. However, the distribution of added carbon across different soil organic carbon fractions is still not well understood. A meta-analysis of 49 studies showed that cover cropping significantly increased both particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) concentrations and stocks, with POC being more responsive than MAOC. This information can guide future efforts in carbon sequestration and sustainable agriculture.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Soil Science
Qingyin Shang, Chen Cheng, Jianjun Wang, Kang Luo, Yongjun Zeng, Xiuxia Yang
Summary: This study examined the effects of different tillage methods on rice production in China and found that reduced tillage can increase yields, reduce CH4 emissions, and decrease NGWP, making it a promising practice.
SOIL & TILLAGE RESEARCH
(2021)
Article
Soil Science
Ihsan Muhammad, Jun Wang, Upendra M. Sainju, Shaohong Zhang, Fazhu Zhao, Ahmad Khan
Summary: Cover crops enhance soil microbial community biomass and affect community structure compared to no cover crops, with responses varying depending on soil type, climatic conditions, and cover crop types. Incorporating cover crop residue into the soil can increase certain microbial parameters but decrease others.
Article
Agronomy
Guanru Lu, Zhonghui Feng, Yang Xu, Yangyang Jin, Guohui Zhang, Jiafeng Hu, Tianhe Yu, Mingming Wang, Miao Liu, Haoyu Yang, Weiqiang Li, Zhengwei Liang
Summary: This study examines the effects of phosphogypsum application on the physicochemical properties and microbial community of saline-alkali soil. The results demonstrate that phosphogypsum significantly improves soil properties, reducing salinity and alkalinity while enhancing nutrient structure and increasing the utilization efficiency of carbon, nitrogen, and phosphorus. Phosphogypsum also significantly improves fungal community diversity, primarily influenced by soil water content, total organic carbon, soil organic matter, total nitrogen, and sodium ion. The findings indicate that combining rice planting with phosphogypsum application effectively modifies saline-alkali soil, regulates fungal community structure, and enhances long-term soil health.
Article
Soil Science
Paul L. Mudge, Jamie Millar, Jack Pronger, Alesha Roulston, Veronica Penny, Scott Fraser, Andre Eger, Thomas Caspari, Balin Robertson, Norman W. H. Mason, Louis A. Schipper
Summary: The study found that irrigation in New Zealand significantly reduced soil carbon and nitrogen stocks, with greater losses observed at greater durations of irrigation and lower aridity levels. The impact of irrigation on soil C and N was negatively related to aridity, with increasingly significant carbon losses observed at sites with higher precipitation levels. The results suggest that a new equilibrium may be reached with lower carbon stocks in irrigated grasslands compared to unirrigated grasslands.
Article
Green & Sustainable Science & Technology
Vladimir Ivezic, Klaus Lorenz, Rattan Lal
Summary: Population growth and increasing food demand contribute to soil degradation and decrease in soil organic carbon (SOC) stock in agriculture. Agroforestry systems like alley cropping are gaining attention for their potential to maintain and increase SOC in agroecosystems. This study aimed to expand knowledge on SOC in alley cropping systems by conducting a meta-analysis and evaluating the impact of introducing trees into agricultural landscapes. Results suggest that beneficial effects on SOC are observed approximately ten years after adopting alley cropping practices. Moreover, the effect of alley cropping is more pronounced in regions with lower initial SOC concentration and in tropical regions compared to temperate zones.
Article
Plant Sciences
Bahareh Hashemi, Hamid Salehian, Mohammad Rezvani, Saeid Soltani
Summary: The way chemicals affect soil biological properties, including enzymatic activities, can reveal the soil's potential to maintain biochemical processes and soil fertility. This research investigated how soil type and depth, as well as the rate and application time of the pretilachlor herbicide, influenced soil biological properties in paddy fields in Babol, Iran. The results showed that soil organic matter content played a role in mitigating the herbicide's effects on soil biological activities and that deeper soil depths had lower biological activities. The use of the herbicide generally increased soil biological activities, except for urease activities, and was linearly related to soil depth. Soil microbial biomass was found to be a more suitable indicator for estimating soil microbial respiration. Soil organic matter can reduce the toxicity of pretilachlor on soil biological activities.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2023)
Article
Green & Sustainable Science & Technology
Jong-Mun Lee, Hyun-Cheol Jeong, Hyo-Suk Gwon, Hyoung-Seok Lee, Hye-Ran Park, Guen-Sik Kim, Do-Gyun Park, Sun-Il Lee
Summary: Previous global meta-analyses on biochar showed inconsistent effects on methane emissions and crop yields. In this study, a meta-analysis of 43 published papers was conducted, revealing that biochar application significantly reduced methane emissions, increased soil organic carbon content, and improved crop yield. The influential factors on methane emissions, soil organic carbon content, and crop yield were identified. These findings provide a scientific basis for biochar application in East Asian rice paddies.
Article
Soil Science
Eric Potash, Kaiyu Guan, Andrew J. Margenot, Dokyoung Lee, Arvid Boe, Michael Douglass, Emily Heaton, Chunhwa Jang, Virginia Jin, Nan Li, Rob Mitchell, Nictor Namoi, Marty Schmer, Sheng Wang, Colleen Zumpf
Summary: Estimating soil organic carbon (SOC) stocks in agricultural fields is crucial for various purposes. Stratified sampling and doubly balanced sampling are two commonly used methods for this task. By comparing the efficiency of these methods, this study found that doubly balanced sampling consistently requires a smaller sample size and can be improved by utilizing readily-available data. Overall, this study provides guidance for more efficient estimation of SOC stocks in agricultural fields.
Article
Environmental Sciences
Zhengjun Yan, Jie Zhou, Lei Yang, Anna Gunina, Yadong Yang, Leanne Peixoto, Zhaohai Zeng, Huadong Zang, Yakov Kuzyakov
Summary: Understanding the sequestration of carbon and nitrogen in diversified cropping systems is crucial for soil health management. A field experiment comparing three cropping systems found that diversified systems increased soil aggregation and stability, leading to higher carbon and nitrogen stocks. Different fractionation methods were used to evaluate soil aggregates, and it was determined that a combination of dry and optimal-moisture sieving is the preferred method to assess aggregate stability.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Agriculture, Multidisciplinary
Esben Oster Mortensen, Chiara De Notaris, Leanne Peixoto, Jorgen E. Olesen, Jim Rasmussen
Summary: Cover crops play a crucial role in increasing soil fertility and mitigating climate change through nutrient recycling and organic matter buildup. A study on the short-term effects of incorporating winter vetch into a cover crop mixture found that higher soil fertility led to a significant reduction in relative net phyllo- and rhizodeposition, despite an increase in cover crop biomass. Adjusting for unrecovered root fragments significantly reduced the estimated phyllo- and rhizodeposition, highlighting that many previous estimates may have been overestimated. Autumn cover crop usage provides a key opportunity for carbon storage, with both aboveground biomass input and belowground carbon investment being important factors.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Geosciences, Multidisciplinary
Marcus Schiedung, Rin-Luca Belle, Avni Malhotra, Samuel Abiven
Summary: High-latitude soils store a large amount of global soil organic carbon (SOC). This study sampled and analyzed mineral forest soils in the Canadian Boreal and Taiga Plain, finding that continuous permafrost conditions have higher SOC stocks compared to discontinuous and sporadic permafrost conditions. The combination of mid-infrared spectroscopy and PLSR modeling was able to accurately predict SOC stocks.
Article
Agriculture, Multidisciplinary
Yajun Peng, Elizabeth L. Rieke, Inderjot Chahal, Charlotte E. Norris, Ken Janovicek, Jeffrey P. Mitchell, Kraig L. Roozeboom, Zachary D. Hayden, Jeffrey S. Strock, Stephen Machado, Virginia R. Sykes, Bill Deen, Oscar Banuelos Tavarez, Audrey V. Gamble, Kate M. Scow, Daniel C. Brainard, Neville Millar, Gregg A. Johnson, Robert R. Schindelbeck, Kirsten S. M. Kurtz, Harold van Es, Sandeep Kumar, Laura L. Van Eerd
Summary: This study used data from the North American Project to Evaluate Soil Health Measurements to explore the impact of cover crops on soil organic carbon (SOC) stocks. The results showed that cover crops significantly improved several indicators of soil health, with non-legumes having a greater impact on SOC accumulation. Integrating non-legume cover crops into diverse crop rotation is likely to be a promising strategy to maximize SOC stocks across North America.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Biochemical Research Methods
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
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
Virology
Fan Zhang, Andrew Gia, Guowei Chen, Lan Gong, Jason Behary, Georgina L. Hold, Amany Zekry, Xubo Tang, Yanni Sun, Emad El-Omar, Xiao-Tao Jiang
Summary: Viruses are abundant and important in ecosystems, and the two methods of whole genome shotgun metagenome and viral-like particle enriched metagenome sequencing are commonly used for comparing viruses in different environments. In this study, both methods were applied to investigate the stool virome in HCC patients and healthy controls, and they both successfully identified altered viral profiles in HCC patients. Ultra-deep sequencing recovered more viruses, and VLPM method can detect RNA viruses. Using both methods would capture different parts of the total virome and identify shared and specific viral signatures.
Article
Agriculture, Multidisciplinary
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
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.
Article
Medicine, General & Internal
Jonathan Daniel Ip, Allen Wing-Ho Chu, Wan-Mui Chan, Rhoda Cheuk-Ying Leung, Syed Muhammad Umer Abdullah, Yanni Sun, Kelvin Kai -Wang To
Summary: This study aimed to estimate the global prevalence of 3CLpro inhibitor-resistant SARS-CoV-2 strains. Analysis of 13.4 million sequences revealed that 0.5% of the sequences contained mutations associated with resistance to nirmatrelvir or ensitrelvir. However, resistance to 3CLpro inhibitors is currently rare.
Article
Materials Science, Multidisciplinary
Huiqiang Hu, Zheng Zhao, Yanni Sun, Jiawei Zhao, Zhengqian Chen, Jianyi Li, Weiqing Kong, Yukun Du, Jiale Shao, Xiaoyang Zhu, Hongbo Lan, Yongming Xi
Summary: This study utilized melt-extrusion 3D printing to prepare biodegradable composite scaffolds, containing bioactive glass, calcium sulfate hemihydrate, and polylactic acid. The compressive strength of scaffolds was comparable to that of human bone tissue, and in vitro and in vivo experiments demonstrated good biocompatibility. The scaffold maintained biomechanical stability of bone defects for 20 weeks without causing liver or kidney damage in animal experiments. Scaffold degradation was accompanied by trabecular bone and vessel neogenesis. The PLA-CSH-BAG group exhibited satisfactory bone defect repair effect compared to the PLA and control groups. In conclusion, the biodegradable porous scaffold is proposed as a safe and effective approach for bone defect repair.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Multidisciplinary
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.
Article
Biochemical Research Methods
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.
Article
Biochemical Research Methods
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
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
Chemistry, Multidisciplinary
Yu-an Li, Yanni Sun, Yuqin Zhang, Quan Li, Shifeng Wang, Roy Curtiss, Huoying Shi
Summary: The development of a Salmonella mRNA interferase regulation vector (SIRV) system is reported in this study, which overcomes the challenge of effective release strategies in engineered vector-based in vivo protein delivery platforms. The SIRV system induces self-lysis for the release of foreign antigens and activates the cytosolic surveillance cGAS-STING axis. It shows improved safety and immunogenicity in mouse and pig models, leading to better survival rates against Streptococcus suis.
Article
Microbiology
Herui Liao, Yongxin Ji, Yanni Sun
Summary: In this study, a new strain-level composition analysis tool named StrainScan is introduced, which employs a novel tree-based k-mers indexing structure to strike a balance between strain identification accuracy and computational complexity. Extensive testing on simulated and real sequencing data shows that StrainScan outperforms popular strain-level analysis tools in terms of accuracy and resolution. It provides more informative strain composition analysis in one sample or across multiple samples.
Article
Biochemical Research Methods
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
Soil Science
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)
