Journal of Microbiology

Journal Articles

Effects of Continuous Straw Returning on Soil Functional Microorganisms and Microbial Communities: Yunpeng Guan , Meikang Wu , Songhao Che , Shuai Yuan , Xue Yang , Siyuan Li , Ping Tian , Lei Wu , Meiying Yang , Zhihai Wu; J. Microbiol. 2023;61(1):49-62. Published online January 26, 2023; DOI: https://doi.org/10.1007/s12275-022-00004-6

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This study examined the changes in soil enzymatic activity, microbial carbon source metabolic diversity, and straw decomposition rates in paddy fields treated with 1, 2, or 3 years of straw returning (SR1–SR3). The soil’s ability to decompose straw and cellulolytic bacteria increased with the number of treatment years (1: 31.9% vs. 2: 43.9% vs. 3: 51.9%, P < 0.05). The numbers of Azotobacter, Nitrobacteria, cellulolytic bacteria, and inorganic phosphate bacteria increased progressively with the numbers of straw returning years. Cellulolytic bacteria and inorganic phosphate bacteria were significantly positively correlated with the decomposition rate (r = 0.783 and r = 0.375, P < 0.05). Based on 16S sequencing results, straw returning improved the microbial diversity of paddy soils by increasing unclassified bacteria and keeping dominant soil microorganism populations unchanged. The relative importance of individual microbial taxa was compared using random forest models. Proteobacteria, ammoniating bacteria, and potassium dissolving bacteria contributed to peroxidase activity. The significant contributors to phosphate monoesterase were Acidobacteriota, Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria. Proteobacteria, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to urease activity. Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to the neutral invertase activity. In conclusion, soil microbial community structure and function were affected within 2 years of straw returning, which was driven by the combined effects of soil organic carbon, available nitrogen, available potassium, and pH. With elapsing straw returning years, soil properties interacted with soil microbial communities, and a healthier soil micro-ecological environment would form.

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The role of tillage practices in wheat straw decomposition and shaping the associated microbial communities in Endocalcaric– Epigleyic Cambisol soil
Arman Shamshitov, Gražina Kadžienė, Francesco Pini, Skaidrė Supronienė
Biology and Fertility of Soils.2025; 61(2): 211. CrossRef
Impact of straw returning on soil ecology and crop yield: A review
Vincent Ninkuu, Zhixin Liu, Aizhi Qin, Yajie Xie, Xiao Song, Xuwu Sun
Heliyon.2025; 11(2): e41651. CrossRef
The different pathways of microbial regulation of organic carbon turnover in the topsoil and subsoil of coastal saline soil after long-term stubble return and subsoiling
Xunya Su, Le Zhang, Hao Meng, Jiaxue Zhao, Han Wang, Lunxiao Shang, Qiyuan Guo, Yupeng Xing, Xianliang Song, Xuezhen Sun, Xiaopei Zhang, Xiaoli Tian, Lili Mao
Applied Soil Ecology.2025; 208: 105970. CrossRef
Synergistic Effects of Rice Straw Return and Nitrogen Fertilizer on Rhizosphere Bacterial Communities and Soil Fertility
Nasita Rahman Borny, Golam Mohammod Mostakim, Asif Raihan, Md Shoaibur Rahman
Journal of Soil, Plant and Environment.2024; : 41. CrossRef
Vertical differences in carbon metabolic diversity and dominant flora of soil bacterial communities in farmlands
Bufan Zheng, Zhipeng Xiao, Jiaqi Liu, Yi Zhu, Kaifeng Shuai, Xiaye Chen, Yongjun Liu, Ruiwen Hu, Guangjue Peng, Junlin Li, Yichao Hu, Zan Su, Ming Fang, Juan Li
Scientific Reports.2024;[Epub] CrossRef
Microbial Network Complexity Helps to Reduce the Deep Migration of Chemical Fertilizer Nitrogen Under the Combined Application of Varying Irrigation Amounts and Multiple Nitrogen Sources
Taotao Chen, Erping Cui, Yanbo Zhang, Ge Gao, Hao You, Yurun Tian, Chao Hu, Yuan Liu, Tao Fan, Xiangyang Fan
Agriculture.2024; 14(12): 2311. CrossRef
Effects of Combined Peanut Shell and Biochar Application on Soil Nutrient Content, CO2 Emission, and Bacterial Community in Dryland Red Soil of Southern China
Xinyi Yu, Qian Wei, Meng Na, Chunjie Tian, Shangqi Xu, Jihai Zhou
Journal of Soil Science and Plant Nutrition.2024; 24(1): 219. CrossRef
Long-term in situ straw returning increased soil aggregation and aggregate associated organic carbon fractions in a paddy soil
Jiaren Liu, Xuehai Wang, Hu Zhang, Yifei Lu, Yusef Kianpoor Kalkhajeh, Hongxiang Hu, Jieying Huang
Heliyon.2024; 10(11): e32392. CrossRef
Agricultural ecosystems rather than fertilization strategies drives structure and composition of the ureolytic microbial functional guilds
Na Lv, Ping Gong, Hao Sun, Xiangxin Sun, Zhiguang Liu, Xueshi Xie, Yan Xue, Yuchao Song, Kaikuo Wu, Tingting Wang, Zhijie Wu, Lili Zhang
Journal of Environmental Management.2024; 372: 123148. CrossRef
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Feng Wu, Xuefang Feng, Xuemei Liu, Di Wu, Songmei Zai, Linbao Liu
Agriculture.2024; 14(2): 287. CrossRef
Improving Soil Quality and Crop Yields Using Enhancing Sustainable Rice Straw Management Through Microbial Enzyme Treatments
Van-Phuc Dinh, Hoai-An Tran-Vu, Thanh Tran, Bich-Ngoc Duong, Ngoc-Mai Dang-Thi, Hoai-Luan Phan-Van, Tuan-Kiet Tran, Van-Hieu Huynh, Thi-Phuong-Tu Nguyen, Thanh Q Nguyen
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Improvement of Saline–Alkali Soil and Straw Degradation Efficiency in Cold and Arid Areas Using Klebsiella sp. and Pseudomonas sp.
Xiaoyu Zhao, Xiaofang Yu, Julin Gao, Jiawei Qu, Qinggeer Borjigin, Tiantian Meng, Dongbo Li
Agronomy.2024; 14(11): 2499. CrossRef
Successive Years of Rice Straw Return Increased the Rice Yield and Soil Nutrients While Decreasing the Greenhouse Gas Intensity
Meikang Wu, Min Nuo, Zixian Jiang, Ruiyao Xu, Hongcheng Zhang, Xiao Lu, Liqun Yao, Man Dou, Xu Xing, Xin Meng, Dongchao Wang, Xiaoshuang Wei, Ping Tian, Guan Wang, Zhihai Wu, Meiying Yang
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Miaomiao Zhang, Pengfei Dang, Bart Haegeman, Xiaoqing Han, Xiaofan Wang, Xuan Pu, Xiaoliang Qin, Kadambot H.M. Siddique
Soil Biology and Biochemistry.2024; 195: 109484. CrossRef
Dissolved Organic Matters, an Intermediary of the Microbial Community and Potassium Fertilizers in A. carmichaeli rhizosphere Soil
Fei Xia, Meng Fu, Chen Liu, Yulong Li, Yi Qiang, Ding He, Guoyan Zhang, Langjun Cui
Journal of Soil Science and Plant Nutrition.2024; 24(3): 5472. CrossRef
Effects of Straw and Nitrogenous Fertilizers on the Soil Aggregate Stability and Quality in Subtropical Regions of China
Jia Yi Yang, Shahbaz Atta Tung, Jin Ting Xu, Yan Qiong Pan, Li Yang, Xun Bo Zhou
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Yaxin Liu, Meng Wu, Jia Liu, Daming Li, Xiaoli Liu, Ling Chen, Xi Guo, Ming Liu
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Effects of Different Tillage Measures Combined with Straw Returning on Soil Enzyme Activity and Microbial Community Structure and Diversity
Sa Xiao, Bing Li, Tingting Zhang, Jianzhu Luo, Jie Wang, Xiangqian Zhang, Juan Li, Dejian Zhang
Agriculture.2024; 15(1): 56. CrossRef
Straw Returning Measures Enhance Soil Moisture and Nutrients and Promote Cotton Growth
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Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model: Katherine D. Mueller , Hao Zhang , Christian R. Serrano , R. Blake Billmyre , Eun Young Huh , Philipp Wiemann , Nancy P. Keller , Yufeng Wang , Joseph Heitman , Soo Chan Lee; J. Microbiol. 2019;57(6):509-520. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8682-x

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Abstract

Mucor circinelloides is a pathogenic fungus and etiologic agent of mucormycosis. In 2013, cases of gastrointestinal illness after yogurt consumption were reported to the US FDA, and the producer found that its products were contaminated with Mucor. A previous study found that the Mucor strain isolated from an open contaminated yogurt exhibited virulence in a murine systemic infection model and showed that this strain is capable of surviving passage through the gastrointestinal tract of mice. In this study, we isolated another Mucor strain from an unopened yogurt that is closely related but distinct from the first Mucor strain and subsequently examined if Mucor alters the gut microbiota in a murine host model. DNA extracted from a ten-day course of stool samples was used to analyze the microbiota in the gastrointestinal tracts of mice exposed via ingestion of Mucor spores. The bacterial 16S rRNA gene and fungal ITS1 sequences obtained were used to identify taxa of each kingdom. Linear regressions revealed that there are changes in bacterial and fungal abundance in the gastrointestinal tracts of mice which ingested Mucor. Furthermore, we found an increased abundance of the bacterial genus Bacteroides and a decreased abundance of the bacteria Akkermansia muciniphila in the gastrointestinal tracts of exposed mice. Measurements of abundances show shifts in relative levels of multiple bacterial and fungal taxa between mouse groups. These findings suggest that exposure of the gastrointestinal tract to Mucor can alter the microbiota and, more importantly, illustrate an interaction between the intestinal mycobiota and bacteriota. In addition, Mucor was able to induce increased permeability in epithelial cell monolayers in vitro, which might be indicative of unstable intestinal barriers. Understanding how the gut microbiota is shaped is important to understand the basis of potential methods of treatment for gastrointestinal illness. How the gut microbiota changes in response to exposure, even by pathogens not considered to be causative agents of food-borne illness, may be important to how commercial food producers prevent and respond to contamination of products aimed at the public. This study provides evidence that the fungal microbiota, though understudied, may play an important role in diseases of the human gut.

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