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Chen K, Jin Z, Zhu Q, Hu X, Tian S, Wang Y, Sun Y, Yuan M, Yao H. Impacts of biodegradable microplastics on rhizosphere bacterial communities of Arabidopsis thaliana: Insights into root hair-dependent colonization. ENVIRONMENTAL RESEARCH 2025; 276:121496. [PMID: 40157415 DOI: 10.1016/j.envres.2025.121496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 03/20/2025] [Accepted: 03/27/2025] [Indexed: 04/01/2025]
Abstract
Biodegradable microplastics (MPs) affect plant health by altering rhizosphere microbial communities. Root hairs create a unique niche for diverse microbes, but the effects of biodegradable MPs on root hair-dependent bacterial colonization are unclear, particularly the direct relationship between microbes in the rhizosphere and bulk soil. Here, the effects of polybutylene adipate terephthalate (PBAT) MPs on root hair-dependent bacterial colonization and diversity in the rhizosphere were revealed using an absolute quantitative method and in-situ zymography with two genotypes of Arabidopsis thaliana (long root hair, wild-type, WT and short root hair, rop2-1 mutant, ROP). The results showed that rhizosphere enzyme activity hotspots, bacterial diversity, and colonization increased from ROP to WT plants. PBAT MPs reduced root hair-dependent bacterial colonization and β-glucosidase hotspots by 17.1 % and 9.8 %, respectively. Despite increasing bacterial absolute abundance in both rhizosphere and bulk soil, PBAT MPs diminished bacterial community modularity and shifted bacterial life strategies from K- to r-strategy via elevated rRNA (rrn) copy numbers and copiotroph/oligotroph ratio. This study indicated that PBAT MPs decreased root hair-dependent bacterial colonization and diversity in the rhizosphere by altering the microbial life history strategies and increasing copiotrophic abundance. This study explained the effects of PBAT MPs on rhizosphere bacterial colonization and diversity from the perspective of root hairs.
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Affiliation(s)
- Keyi Chen
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Zhihui Jin
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Qing Zhu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Xiaodie Hu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Sijia Tian
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yulin Wang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Yaru Sun
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Ming Yuan
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.
| | - Huaiying Yao
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Microbial Transformation and Regulation of Biogenic Elements in the Middle Reaches of the Yangtze River, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo, China.
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Jiang SY, Shen KW, Brandón MG, Lu SB, Tomberlin JK, Tang XT, Wang H, Xiang FM, Chen XX, Zhang ZJ. Using black soldier fly larval frass to restore soil health. BIORESOURCE TECHNOLOGY 2025; 432:132701. [PMID: 40398567 DOI: 10.1016/j.biortech.2025.132701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 05/02/2025] [Accepted: 05/16/2025] [Indexed: 05/23/2025]
Abstract
The importance of sustainable solutions for restoring soil health amidst increasing soil degradation and organic waste accumulation has gained significant attention. Black soldier fly larval (BSFL) bioconversion offers a promising solution by converting organic wastes into value-added products, such as larval biomass and frass. BSFL frass, the main output of the bioconversion, is increasingly recognized for its potential to restore soil health. Here, this paper provides a comprehensive synthesis of BSFL frass production and properties, and explores its role in mitigating multiple problems related to soil degradation. Finally, this paper further discusses the challenges and future directions for the effective, safe, and sustainable use of BSFL frass. In summary, this paper revealed that BSFL frass, with its unique physicochemical properties and a variety of beneficial bioactive compounds and microorganisms, holds the potential to address problems such as soil acidification, fertility degradation, microbial dysbiosis, and soil-borne diseases, thereby restoring soil health.
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Affiliation(s)
- Shuo-Yun Jiang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Ave 688, Hangzhou, Zhejiang Province 310058, China
| | - Ke-Wei Shen
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Ave 688, Hangzhou, Zhejiang Province 310058, China
| | | | - Sheng-Biao Lu
- Yangtze River Delta Health Agriculture Research Institute, Tongxiang Economic HiTech Zone, Tongxiang 314500, China
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, 2475 TAMU, College Station, TX 77843, USA
| | - Xiao-Tian Tang
- Zhejiang Key Laboratory of Biology and Ecological Regulation of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology Zhejiang University, Hangzhou, China
| | - Hang Wang
- Yunnan Key Laboratory of Plateau Wetland Conversion, Restoration and Ecological Services, National Plateau Wetland Research Center, Southwest Forestry University, Kunming 650224, China
| | - Fang-Ming Xiang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Ave 688, Hangzhou, Zhejiang Province 310058, China
| | - Xue-Xin Chen
- Department of Entomology, Texas A&M University, 2475 TAMU, College Station, TX 77843, USA
| | - Zhi-Jian Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Yuhangtang Ave 688, Hangzhou, Zhejiang Province 310058, China.
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Quan Y, Gan X, Lu S, Shi X, Bai M, Lin Y, Gou Y, Zhang H, Zhang X, Wei J, Chang T, Li J, Liu J. The relict plant Tetraena mongolica plantations increase the nutrition and microbial diversity in desert soil. FRONTIERS IN PLANT SCIENCE 2025; 16:1539336. [PMID: 40182555 PMCID: PMC11965594 DOI: 10.3389/fpls.2025.1539336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 02/25/2025] [Indexed: 04/05/2025]
Abstract
Introduction Tetraena mongolica was established in the West Ordos Region of northwest China approximately 140 million years ago. It plays an irreplaceable role in maintaining local ecosystem stability. Methods This study aimed to evaluate the effects of planting T. mongolica on soil nutrition and microbial communities by comparing the root zone soil (Rz_soil) and bare soil (B_soil) across three different plant communitie. Results The results showed that T. mongolica decreased soil pH and Na+ while increasing available potassium, soil organic matter, organic carbon, total nitrogen, and potassium. T. mongolica significantly improved the diversity indices (Sobs and Ace), as well as the richness index (Chao), of bacterial and fungal communities across three plant communities. Meanwhile, the relative abundances of Rubrobacter and norank_c_Actinobacteria in the bacterial communities declined significantly in the Rz_soil compared with the B_soil across all three plant communities. In contrast, the relative abundances of Fusarium and Penicillium were higher, whereas those of Monosporascus and Darksidea were lower in Rz_soil than in B_soil in the two plant communities. T. mongolica decreased the soil bacterial co-occurrence networks while increasing the soil fungal co-occurrence networks. Discussion These results provide a new perspective to understand the role of T. Mongolica in the desert ecosystems.
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Affiliation(s)
- Yanan Quan
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Xiuwen Gan
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Shiyun Lu
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Xiaodong Shi
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Mingsheng Bai
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Yin Lin
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Yufei Gou
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Hong Zhang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Xinyue Zhang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Jiayuan Wei
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Tianyu Chang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Jingyu Li
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
| | - Jianli Liu
- College of Biological Science and Engineering, North Minzu University, Yinchuan, Ningxia, China
- Key Laboratory of Ecological Protection of Agro-pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People’s Republic of China, Yinchuan, Ningxia, China
- Ningxia Key Laboratory of Microbial Resources Development and Applications in Special Environment, Science and Technology Department of Ningxia, Yinchuan, Ningxia, China
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Wang J, Song M, Yao L, Li P, Si E, Li B, Meng Y, Ma X, Yang K, Zhang H, Shang X, Wang H. Metagenomic analysis reveal the phytoremediation effects of monocropping and intercropping of halophytes Halogeton glomeratus and Suaeda glauca in saline soil of Northwestern China. BMC PLANT BIOLOGY 2025; 25:213. [PMID: 39966722 PMCID: PMC11834545 DOI: 10.1186/s12870-025-06225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 02/07/2025] [Indexed: 02/20/2025]
Abstract
AIMS Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved. MATERIALS AND METHODS Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics. RESULTS After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation. CONCLUSIONS Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China.
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Affiliation(s)
- Juncheng Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Meini Song
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Lirong Yao
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Pengcheng Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Erjing Si
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaxiong Meng
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xiaole Ma
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Ke Yang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Hong Zhang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Huajun Wang
- State Key Lab of Aridland Crop Science / Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou, China.
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou, China.
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Wang C, Yang Y, Xu X, Wang D, Shi X, Liu L, Deng Y, Li L, Zhang T. The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards. MICROBIOME 2025; 13:26. [PMID: 39871306 PMCID: PMC11773863 DOI: 10.1186/s40168-024-02009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 12/17/2024] [Indexed: 01/29/2025]
Abstract
BACKGROUND High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analytical microbiology, enabling characterization of community dynamics and assessing microbial pollutants for the development of intervention strategies. However, the relative abundances derived from sequencing impede comparisons across samples and studies. RESULTS This review systematically summarizes various absolute quantification (AQ) methods and their applications to obtain the absolute abundance of microbial cells and genetic elements. By critically comparing the strengths and limitations of AQ methods, we advocate the use of cellular internal standard-based high-throughput sequencing as an appropriate AQ approach for studying environmental microbiome originated from samples of complex matrices and high heterogeneity. To minimize ambiguity and facilitate cross-study comparisons, we outline essential reporting elements for technical considerations, and provide a checklist as a reference for environmental microbiome research. CONCLUSIONS In summary, we propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology, and we anticipate that this approach will greatly benefit future studies. Video Abstract.
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Affiliation(s)
- Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Xiaoqing Xu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Xianghui Shi
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Department of Science and Environmental Studies, The Education University of Hong Kong, 10 Lo Ping Road, Tai Po, New Territories, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China.
- School of Public Health, The University of Hong Kong, Hong Kong, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China.
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Xu D, Zhang X, Liu J, Zhang Z, Qin C, Zhao Y, Wu G, Wu N, Xu W. Synergistic Remediation of Cadmium Pollution in Saline-Alkali Soil by Hydrogel and Suaeda salsa. ACS APPLIED MATERIALS & INTERFACES 2025; 17:3911-3923. [PMID: 39762154 DOI: 10.1021/acsami.4c18057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
Abstract
The cadmium (Cd) in saline-alkali soil poses a serious threat to the ecological environment and human health. Suaeda salsa, as a hyperaccumulator plant, can remediate Cd in saline-alkali soil, but the efficiency of phytoremediation is low. To improve the remediation effect of Cd pollution in saline-alkali soil, this study for the first time uses the synergy of hydrogel and Suaeda salsa for the remediation of Cd in saline-alkali soil. Hydrogel possesses excellent mechanical properties and outstanding adsorption properties. In addition, the hydrogel increases the content of some nutrient elements in the soil and improves the physicochemical properties of the soil. The water retention capacity of the hydrogel and the improvement of the physicochemical properties of the soil further promote the growth of Suaeda salsa. Meanwhile, both the hydrogel and Suaeda salsa have a positive impact on microorganisms. Our experiment provides a brand-new way for the remediation of Cd pollution in saline-alkali soil and is of great significance for soil health and ecological protection.
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Affiliation(s)
- Deliang Xu
- School of Resources and Environmental Engineering, Ludong University, Yantai 264025, China
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Xinbin Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Jiahui Liu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Zhen Zhang
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Chao Qin
- School of Resources and Environmental Engineering, Ludong University, Yantai 264025, China
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
| | - Ying Zhao
- College of Water Conservancy and Civil Engineering, Ludong University, Yantai 264025, China
| | - Guochao Wu
- Modern Seed Industry and Green Breeding Research Center, College of Horticulture, Ludong University, Yantai 264025, China
| | - Nan Wu
- School of Resources and Environmental Engineering, Ludong University, Yantai 264025, China
| | - Wenlong Xu
- School of Chemistry and Materials Science, Ludong University, Yantai 264025, China
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7
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Yao Y, Wang L, Zhai H, Dong H, Wang J, Zhao Z, Xu Y. Bacillus velezensis A-27 as a potential biocontrol agent against Meloidogyne incognita and effects on rhizosphere communities of celery in field. Sci Rep 2025; 15:1057. [PMID: 39774715 PMCID: PMC11707364 DOI: 10.1038/s41598-024-83687-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Accepted: 12/16/2024] [Indexed: 01/11/2025] Open
Abstract
Meloidogyne incognita, a highly destructive plant-parasitic nematode, poses a significant threat to crop production. The reliance on chemical nematicides for nematode control has been crucial; however, the banning of many effective nematicides due to their adverse effects has necessitated the exploration of alternative solutions. Rhizosphere biocontrol bacteria, particularly strains of Bacillus, have demonstrated promising results in managing plant-parasitic nematodes. In this study, strain A-27 was identified as Bacillus velezensis based on its morphological, physiological, and molecular characteristics, including 16 S rRNA and gyrA sequencing. Strain A-27 exhibited high larvicidal and ovicidal efficacy in vitro, with estimated LC50 values of 4.0570 × 108 CFU/mL for larvicidal efficacy and 3.6464 × 108 CFU/mL for ovicidal efficacy. In a pot experiment, B. velezensis A-27 significantly reduced the root gall index, achieving a control efficacy of 85.36%. Field experiments further indicated that A-27 reduced the root gall index with a control efficacy of 67.31%, while also decreasing the J2 population density of M. incognita and significantly enhancing the growth of celery plants. Additionally, high-throughput sequencing analysis revealed that B. velezensis A-27 significantly increased the relative abundances of Bacillus and Sphingomonas, while markedly reducing the relative abundances of Fusarium, Mortierella, and Cephaliophora in the celery rhizosphere. These findings suggest that B. velezensis A-27 has potential as an effective biocontrol agent against M. incognita, offering a promising alternative to chemical nematicides in sustainable agriculture.
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Affiliation(s)
- Yanan Yao
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Liyi Wang
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Haozhen Zhai
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Hailong Dong
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Jianming Wang
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China
| | - Zengqi Zhao
- Auckland Mail Centre, Manaaki Whenua-Landcare Research, Private Bag 92170, Auckland, 1142, New Zealand
| | - Yumei Xu
- Laboratory of Nematology, Department of Plant Pathology, College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, China.
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Asghar W, Craven KD, Swenson JR, Kataoka R, Mahmood A, Farias JG. Enhancing the Resilience of Agroecosystems Through Improved Rhizosphere Processes: A Strategic Review. Int J Mol Sci 2024; 26:109. [PMID: 39795965 PMCID: PMC11720004 DOI: 10.3390/ijms26010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 12/18/2024] [Accepted: 12/25/2024] [Indexed: 01/13/2025] Open
Abstract
As farming practices evolve and climate conditions shift, achieving sustainable food production for a growing global population requires innovative strategies to optimize environmentally friendly practices and minimize ecological impacts. Agroecosystems, which integrate agricultural practices with the surrounding environment, play a vital role in maintaining ecological balance and ensuring food security. Rhizosphere management has emerged as a pivotal approach to enhancing crop yields, reducing reliance on synthetic fertilizers, and supporting sustainable agriculture. The rhizosphere, a dynamic zone surrounding plant roots, hosts intense microbial activity fueled by root exudates. These exudates, along with practices such as green manure application and intercropping, significantly influence the soil's microbial community structure. Beneficial plant-associated microbes, including Trichoderma spp., Penicillium spp., Aspergillus spp., and Bacillus spp., play a crucial role in improving nutrient cycling and promoting plant health, yet their interactions within the rhizosphere remain inadequately understood. This review explores how integrating beneficial microbes, green manures, and intercropping enhances rhizosphere processes to rebuild microbial communities, sequester carbon, and reduce greenhouse gas emissions. These practices not only contribute to maintaining soil health but also foster positive plant-microbe-rhizosphere interactions that benefit entire ecosystems. By implementing such strategies alongside sound policy measures, sustainable cropping systems can be developed to address predicted climate challenges. Strengthening agroecosystem resilience through improved rhizosphere processes is essential for ensuring food security and environmental sustainability in the future. In conclusion, using these rhizosphere-driven processes, we could develop more sustainable and resilient agricultural systems that ensure food security and environmental preservation amidst changing climate situations.
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Affiliation(s)
- Waleed Asghar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (K.D.C.); (J.R.S.)
| | - Kelly D. Craven
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (K.D.C.); (J.R.S.)
| | - Jacob R. Swenson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA; (K.D.C.); (J.R.S.)
| | - Ryota Kataoka
- Department of Environmental Sciences, Faculty of Life & Environmental Sciences, University of Yamanashi, Yamanashi 400-0016, Japan;
| | - Ahmad Mahmood
- Departments of Climate Change and Soil and Environmental Sciences, Muhammad Nawaz Shareef-University of Agriculture, Multan 60000, Pakistan;
| | - Júlia Gomes Farias
- USDA-ARS, US Arid Land Agricultural Research Center, 21881 North Cardon Lane Maricopa, Maricopa, AZ 85138, USA;
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Cao J, Zhou H, Wang X, Wang Y, Li Y, Joseph S, Wang X, Sun M, Zhang K, Lin Y, Xu G, Ni K, Shang J, Yang F. Game changer for anaerobic fermentation of paper mulberry: Sucrose-loaded biochar enhancing microbial communities and lactic acid fermentation. BIORESOURCE TECHNOLOGY 2024; 414:131552. [PMID: 39374834 DOI: 10.1016/j.biortech.2024.131552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/23/2024] [Accepted: 09/29/2024] [Indexed: 10/09/2024]
Abstract
This study investigated biochar effects, either alone or combined with sucrose, on fermentation quality, microbial communities, and in vitro rumen digestion of anaerobic fermented paper mulberry. The biochar alkaline functional groups bind to lactic acid, reducing acid inhibition and promoting Lactiplantibacillus proliferation. Owing to the low sugar content of paper mulberry, lactic acid bacteria in the biochar group primarily underwent heterofermentation, resulting in the lowest lactic and highest acetic acid contents. Treated with sucrose-loaded biochar, the increased substrate supported homofermentation, leading to the highest lactic and lowest acetic acid contents, with a 15.0 % increase in lactic acid and a 22.2 % decrease in ammoniacal nitrogen compared with the control after 75 days. In vitro rumen tests showed that the biochar-sucrose group had the highest dry matter degradation rate (45.9 %) and a 24.2 % reduction in methane emissions. Concludingly, sucrose-loaded biochar is recommended as effective for lactic acid production under anaerobic conditions.
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Affiliation(s)
- Jingwen Cao
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hongzhang Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xuekai Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China; College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Yang Wang
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Yu Li
- College of Engineering, China Agricultural University, Beijing, China; Faculty of Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Stephen Joseph
- School of Materials Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xiaorong Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Mengyao Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Keyi Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Yanli Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Gang Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Jianying Shang
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China; College of Animal Science, Guizhou University, Guiyang, China
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10
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He C, Li K, Meng L, Ruan Y, Jia Z. Glucose addition in natural forest soils has higher biological nitrogen fixation capacity than other types of soils. Sci Rep 2024; 14:23909. [PMID: 39397025 PMCID: PMC11471798 DOI: 10.1038/s41598-024-72796-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 09/10/2024] [Indexed: 10/15/2024] Open
Abstract
Land use changes soil microbial and chemical properties, but the mechanism of biological nitrogen fixation under different land use patterns is rarely reported, so we used four types of soil: Natural forest soil (NS), healthy banana soil (HS), diseased banana soil (DS) and paddy soil (PS). Treatments included the control (CK), addition of glucose (G), addition of glucose and ammonium nitrate (GN), addition of banana straw (BS), addition of banana straw and ammonium nitrate (BSN), addition of banana root (BR), and addition of banana root and ammonium nitrate (BRN). The study found that the change of soil utilization types, glucose addition increased carbon dioxide emissions (Compared with the control, increased by 963.11%, 508.39%, 794.77% and 511.34%, respectively) and enhanced the ability of soil microbial nitrogen fixation. Importantly, natural forest soil microorganisms have a higher biological nitrogen fixation capacity compared to other types of soils. Glucose addition caused the accumulation of ammonium nitrogen (Compared with the control, increased by 426.08%, 934.21%, 420% and 1065.95%, respectively), indicating that microorganisms had higher utilization efficiency of soluble carbon and enhanced the biological nitrogen fixation capacity, and nitrogen addition caused the accumulation of ammonium nitrogen, thereby weakening the biological nitrogen fixation capacity. At the same time, glucose significantly increased the Fimicutes phylum (83.73%, 66.38%, 67.18% and 70.36%) and lowered the level of other bacterial phylums, thereby reducing the bacterial network structure, and the stability of the soil environment has decreased. Forest analysis showed that CO2 was an important factor in predicting the bacterial community structure of different soil types, an increase in CO2 content can predict drastic changes in the bacterial community. Bacteria at the Fimicutes phylum level preferred glucose, which may also have a negative effect on bacteria at the level of other phylums.
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Affiliation(s)
- Chen He
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China
| | - Kaikai Li
- Hainan Research Academy of Environmental Sciences, Haikou, China
| | - Lei Meng
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China.
| | - Yunze Ruan
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, China.
| | - Zhongjun Jia
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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11
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Yin H, Hong Q, Yu X, Wang H, Shi X, Liu W, Yuan T, Tu Z. Dynamic changes in volatile profiles and bacterial communities during natural fermentation of Mei yu, traditional Chinese fermented fish pieces. Food Res Int 2024; 194:114882. [PMID: 39232519 DOI: 10.1016/j.foodres.2024.114882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/23/2024] [Accepted: 08/07/2024] [Indexed: 09/06/2024]
Abstract
Microbial metabolism is important for the unique flavor formation of Mei yu, a kind of traditional Chinese fermented fish pieces. However, the interactive relationship between microorganisms and flavor components during fermentation is still unclear. In this study, electronic nose and headspace-solid-phase microextraction-gas chromatography-mass spectrometry analysis were performed to identify flavor components in Mei yu during the fermentation, and the absolute microbial quantification was conducted to identify the diversity and succession of microbial communities. During fermentation, there was an increase in the types of volatile compounds. Alcohols, aldehydes, aromatics and esters were the main flavor compounds and significantly increased in Mei yu, while hydrocarbon and aldehydes significantly decreased. The absolute abundances of Lactobacillus, Lactococcus and Weissella increased significantly after 3 days' fermentation, which were closely associated with the productions of 1-nonanol, 2-methoxy-4-vinylphenol, guaiacol, ethyl palmitate and ethyl caprylate that might though pathways related to fatty acid biosynthesis and amino acid metabolism. However, these genera were negatively correlated with the production of indole. Additionally, the total volatile basic nitrogen (TVB-N) levels of Mei yu fermented during 3 days were within the limits of 25 mg TVB-N/100 g fish, with the contents of free amino acids and lipoxygenase activities were significant lower than that of 4 days' fermentation. In view of food safety and flavor, it suggested that the natural fermented Mei yu at room temperature should be controlled within 3 days. This study highlights the application of absolute quantification to microbiome analysis in traditional fermented Mei yu and provides new insights into the roles of microorganisms in flavor formation during fermentation.
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Affiliation(s)
- Hongmei Yin
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Qiang Hong
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Xiang Yu
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Hui Wang
- College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Xiaodan Shi
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China.
| | - Wei Liu
- Xinjiang Key Laboratory of Clean Conversion and High Value Utilization of Biomass Resources, School of Chemistry and Chemical Engineering, Yili Normal University, Yining, Xinjiang 835000, China
| | - Tao Yuan
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
| | - Zongcai Tu
- School of Health, Jiangxi Normal University, Nanchang, Jiangxi 330022, China; State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, Jiangxi 330047, China.
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12
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Wei L, Wang Y, Li N, Zhao N, Xu S. Bacteria-Like Gaiella Accelerate Soil Carbon Loss by Decomposing Organic Matter of Grazing Soils in Alpine Meadows on the Qinghai-Tibet Plateau. MICROBIAL ECOLOGY 2024; 87:104. [PMID: 39110233 PMCID: PMC11306262 DOI: 10.1007/s00248-024-02414-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024]
Abstract
The alpine meadows of the Qinghai-Tibet Plateau have significant potential for storing soil carbon, which is important to global carbon sequestration. Grazing is a major threat to its potential for carbon sequestration. However, grazing poses a major threat to this potential by speeding up the breakdown of organic matter in the soil and releasing carbon, which may further lead to positive carbon-climate change feedback and threaten ecological security. Therefore, in order to accurately explore the driving mechanism and regulatory factors of soil organic matter decomposition in grazing alpine meadows on the Qinghai-Tibet Plateau, we took the grazing sample plots of typical alpine meadows as the research object and set up grazing intensities of different life cycles, aiming to explore the relationship and main regulatory factors of grazing on soil organic matter decomposition and soil microorganisms. The results show the following: (1) soil microorganisms, especially Acidobacteria and Acidobacteria, drove the decomposition of organic matter in the soil, thereby accelerating the release of soil carbon, which was not conducive to soil carbon sequestration in grassland; (2) the grazing triggering effect formed a positive feedback with soil microbial carbon release, accelerating the decomposition of organic matter and soil carbon loss; and (3) the grazing ban and light grazing were more conducive to slowing down soil organic matter decomposition and increasing soil carbon sequestration.
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Affiliation(s)
- Lin Wei
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
- Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem, Qinghai, China
| | - Yalin Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Na Li
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- College of Resource and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhao
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
- Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem, Qinghai, China.
| | - Shixiao Xu
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China.
- Qinghai Haibei National Field Research Station of Alpine Grassland Ecosystem, Qinghai, China.
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13
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Li J, He P, Jin Q, Chen J, Chen D, Dai X, Ding S, Chu L. Aeration Alleviated the Adverse Effects of Nitrogen Topdressing Reduction on Tomato Root Vigor, Photosynthetic Performance, and Fruit Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1378. [PMID: 38794448 PMCID: PMC11125352 DOI: 10.3390/plants13101378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024]
Abstract
To explore the compensation effect of aeration on tomato vegetative and reproductive growth in arid and semi-arid areas, a two-year field experiment was conducted with four micro-nano aeration ratios (0%, 5%, 10%, and 15%) and three nitrogen topdressing levels (80, 60, and 40 kg·ha-1) during the tomato growth period in Ningxia, China. The results showed that increasing the aeration ratio in the range of 0-15% was conducive to the enhancement of tomato root vigor (the ability of triphenyltetrazolium chloride to be reduced, 3-104%) and the leaf net photosynthetic rate (14-63%), favorable to the facilitation of plant dry matter accumulation (3-59%) and plant nitrogen accumulation (2-70%), and beneficial to the improvement of tomato yield (12-44%) and fruit quality. Interestingly, since the aeration ratio exceeded 10%, the increase in the aeration ratio showed no significant effects on the single-fruit weight, tomato yield, and fruit quality. Moreover, with aerated underground drip irrigation, properly reducing the traditional nitrogen topdressing level (80 kg·ha-1) by 25% was favorable for enhancing tomato root vigor (5-31%), increasing tomato yield (0.5-9%), and improving fruit soluble solid accumulation (2-5%) and soluble sugar formation (4-9%). Importantly, increasing the aeration ratio by 5% could compensate for the adverse effects of reducing the nitrogen topdressing level by 25% by improving the leaf photosynthetic rate, promoting plant dry matter accumulation, increasing tomato yield, and enhancing the soluble solid and soluble sugar accumulation in tomato fruits. Synthetically considering the decrease in the nitrogen topdressing amount, leading to plant growth promotion, a tomato yield increase, and fruit quality improvement, a favorable nitrogen topdressing level of 60 kg·ha-1 and the corresponding proper aeration ratio of 10% were suggested for tomato underground drip irrigation in the Yinbei Irrigation District of Ningxia.
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Affiliation(s)
- Jingang Li
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Pingru He
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Qiu Jin
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing 210029, China
| | - Jing Chen
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Dan Chen
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Xiaoping Dai
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Siyu Ding
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
| | - Linlin Chu
- College of Agricultural Science and Engineering, Hohai University, Nanjing 211100, China; (J.L.)
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14
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Bai X, Zhang E, Wu J, Ma D, Zhang C, Zhang B, Liu Y, Zhang Z, Tian F, Zhao H, Wang B. Soil fungal community is more sensitive than bacterial community to modified materials application in saline-alkali land of Hetao Plain. Front Microbiol 2024; 15:1255536. [PMID: 38374915 PMCID: PMC10875129 DOI: 10.3389/fmicb.2024.1255536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/04/2024] [Indexed: 02/21/2024] Open
Abstract
Soil salinization has become a major challenge that severely threatens crop growth and influences the productivity of agriculture. It is urgent to develop effective management measures to improve saline-alkali soil. Thus, in this study, soil properties, microbial communities, and function under desulfurization gypsum (DE), soil amendment (SA), farm manure (FA), and co-application of desulfurization gypsum, soil amendment, and farm manure (TA) in a field experiment were examined by high-throughput sequencing. The results showed that the application of modified materials is an effective approach in improving saline-alkali soil, especially TA treatment significantly increased the content of available phosphorus (AP), available potassium (AK), soil organic matter (SOM), and alkaline hydrolysis nitrogen (AHN) and decreased pH, bulk density (BD), and electrical conductivity (EC). The application of modified materials resulted in notable enhancement in fungal diversity and altered the composition and structure of the fungal community. Conversely, the effect on the bacterial community was comparatively minor, with changes limited to the structure of the community. Regarding the fungal community composition, Ascomycota, Mortierellomycota, and Basidiomycota emerged as the dominant phyla across all treatments. At each taxonomic level, the community composition exhibited significant variations in response to different modified materials, resulting in divergent soil quality. The TA treatment led to a decrease in Mortierellomycota and an increase in Ascomycota, potentially enhancing the ability to decompose organic matter and facilitate soil nutrient cycling. Additionally, the sensitivity of fungal biomarkers to modified materials surpassed that of the bacterial community. The impact of modified materials on soil microbial communities primarily stemmed from alterations in soil EC, AP, AK, and SOM. FUNGuild analysis indicated that the saprotroph trophic mode group was the dominant component, and the application of modified materials notably increased the symbiotroph group. PICRUSt analysis revealed that metabolism was the most prevalent functional module observed at pathway level 1. Overall, the application of modified materials led to a decrease in soil EC and an increase in nutrient levels, resulting in more significant alterations in the soil fungal community, but it did not dramatically change the soil bacterial community. Our study provides new insights into the application of modified materials in increasing soil nutrients and altering soil microbial communities and functions and provides a better approach for improving saline-alkali soil of Hetao Plain.
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Affiliation(s)
- Xiaolong Bai
- College of Agriculture, Ningxia University, Yinchuan, China
| | - En Zhang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Jinmin Wu
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Donghai Ma
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Chaohui Zhang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Bangyan Zhang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yunpeng Liu
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Zhi Zhang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Feng Tian
- Tumote Right Banner Agricultural Technology Extension Center, Baotou, China
| | - Hui Zhao
- Tumote Right Banner Agricultural Technology Extension Center, Baotou, China
| | - Bin Wang
- College of Agriculture, Ningxia University, Yinchuan, China
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15
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Lima Â, Muzny CA, Cerca N. An Indirect Fluorescence Microscopy Method to Assess Vaginal Lactobacillus Concentrations. Microorganisms 2024; 12:114. [PMID: 38257941 PMCID: PMC10820742 DOI: 10.3390/microorganisms12010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Lactobacillus species are the main colonizers of the vaginal microbiota in healthy women. Their absolute quantification by culture-based methods is limited due to their fastidious growth. Flow cytometry can quantify the bacterial concentration of these bacteria but requires the acquisition of expensive equipment. More affordable non-culturable methods, such as fluorescence microscopy, are hampered by the small size of the bacteria. Herein, we developed an indirect fluorescence microscopy method to determine vaginal lactobacilli concentration by determining the correlation between surface area bacterial measurement and initial concentration of an easily cultivable bacterium (Escherichia coli) and applying it to lactobacilli fluorescence microscopy counts. In addition, vaginal lactobacilli were quantified by colony-forming units and flow cytometry in order to compare these results with the indirect method results. The colony-forming-unit values were lower than the results obtained from the other two techniques, while flow cytometry and fluorescence microscopy results agreed. Thus, our developed method was able to accurately quantify vaginal lactobacilli.
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Affiliation(s)
- Ângela Lima
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
| | - Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
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16
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Lv J, Qi P, Yan X, Bai L, Zhang L. Structure and Metabolic Characteristics of Intestinal Microbiota in Tibetan and Han Populations of Qinghai-Tibet Plateau and Associated Influencing Factors. Microorganisms 2023; 11:2655. [PMID: 38004668 PMCID: PMC10672793 DOI: 10.3390/microorganisms11112655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Residents of the Qinghai-Tibet Plateau might experience shifts in their gut microbiota composition as a result of the plateau environment. For example, high altitudes can increase the abundance of obligate anaerobic bacteria, decrease the number of aerobic bacteria and facultative anaerobic bacteria, increase probiotics, and decrease pathogenic bacteria. This study aimed to determine the structure and metabolic differences in intestinal microbial communities among the Tibetan and Han populations on the Qinghai-Xizang Plateau and shed light on the factors that influence the abundance of the microbial communities in the gut. The structural characteristics of intestinal microorganisms were detected from blood and fecal samples using 16S rRNA sequencing. Metabolic characteristics were detected using gas chromatography-time-of-flight mass spectrometry (GC-TOFMS). The influencing factors were analyzed using Spearman's correlation analysis. Bacteroides and Bifidobacterium were dominant in the intestinal tract of the Han population, while Bacteroides and Prevotella were dominant in that of the Tibetan population, with marked differences in Pseudomonas, Prevotella, and other genera. Ferulic acid and 4-methylcatechol were the main differential metabolites between the Tibetan and Han ethnic groups. This may be the reason for the different adaptability of Tibetan and Han nationalities to the plateau. Alanine aminotransferase and uric acid also have a high correlation with different bacteria and metabolites, which may play a role. These results reveal notable disparities in the compositions and metabolic characteristics of gut microbial communities in the Tibetan and Han people residing on the Qinghai-Tibet Plateau and may provide insights regarding the mechanism of plateau adaptability.
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Affiliation(s)
- Jin Lv
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (J.L.); (P.Q.); (X.Y.); (L.B.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Ping Qi
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (J.L.); (P.Q.); (X.Y.); (L.B.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Xiangdong Yan
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (J.L.); (P.Q.); (X.Y.); (L.B.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Liuhui Bai
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (J.L.); (P.Q.); (X.Y.); (L.B.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Lei Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou 730000, China; (J.L.); (P.Q.); (X.Y.); (L.B.)
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, The First Hospital of Lanzhou University, Lanzhou 730000, China
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17
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Hu G, Cao H, Ye C, Wang F. Effect of cadmium stress on the bacterial community in the rhizosphere of mulberry (Morus alba L.). Braz J Microbiol 2023; 54:2297-2305. [PMID: 37594657 PMCID: PMC10484825 DOI: 10.1007/s42770-023-01090-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
Mulberry has a good tolerance to cadmium (Cd) and is considered a candidate plant for phytoremediation. The rhizosphere microbial community plays an important role in phytoremediation. Nevertheless, little information on the rhizosphere microbial community mechanisms in mulberry during the phytoremediation of Cd-contaminated soil is available. In this study, the remediation efficiency of mulberry in pots subjected to three simulated Cd pollution levels and their rhizosphere bacterial communities during the remediation process were analyzed. "Yuesang 11" was used as the test mulberry variety, and three simulated Cd pollution levels were set by adding three concentrations of Cd (Cd5, 5 mg kg-1; Cd3, 3 mg kg-1; Cd2, 2 mg kg-1). The results showed that the elimination rates of Cd in the rhizosphere soil were 81.7%, 85.3%, and 57.9% under the stress of the Cd2, Cd3, and Cd5 conditions, respectively. Meanwhile, 3,082,583 high-quality sequence reads and 976 operational taxonomic units were successfully obtained from the mulberry rhizosphere soil by high-throughput absolute quantification sequencing and further assigned to 11 bacterial phyla and 26 families. Of these, decreased abundances of 19 bacteria at the family level and increased abundances of seven bacteria under Cd stress were revealed by comparative analysis. Based on the alpha diversity indices (Chaol, Shannon and Simpson) and principal component analysis, the rhizosphere bacterial diversity of the Cd5 condition was significantly decreased, but that of the Cd2 and Cd3 conditions was not different from that of soil without Cd (CK). Likewise, redundancy analysis showed that the abundances of Acidobacteria Gp2, Acidobacteria Gp13, and Sphingobacteria were significantly positively associated with the elimination rates of Cd. This study suggested that the mulberry rhizosphere contains a relatively stable bacterial community consisting of diverse Cd-resistant bacteria, providing a scientific basis for remediating heavy-metal polluted soils using mulberry.
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Affiliation(s)
- Guiping Hu
- Economic Crops Research Institute of Jiangxi Province, Nanchang, 330202, Jiangxi, China.
- Jiangxi Provincial Research Center for Sericultural Engineering and Technology, Nanchang, 330202, China.
| | - Hongmei Cao
- Economic Crops Research Institute of Jiangxi Province, Nanchang, 330202, Jiangxi, China
- Jiangxi Provincial Research Center for Sericultural Engineering and Technology, Nanchang, 330202, China
| | - Chuan Ye
- Economic Crops Research Institute of Jiangxi Province, Nanchang, 330202, Jiangxi, China
- Jiangxi Provincial Research Center for Sericultural Engineering and Technology, Nanchang, 330202, China
| | - Feng Wang
- Economic Crops Research Institute of Jiangxi Province, Nanchang, 330202, Jiangxi, China
- Jiangxi Provincial Research Center for Sericultural Engineering and Technology, Nanchang, 330202, China
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18
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Pang G, Li X, Ding M, Jiang S, Chen P, Zhao Z, Gao R, Song B, Xu X, Shen Q, Cai FM, Druzhinina IS. The distinct plastisphere microbiome in the terrestrial-marine ecotone is a reservoir for putative degraders of petroleum-based polymers. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131399. [PMID: 37062095 DOI: 10.1016/j.jhazmat.2023.131399] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
Research into plastic-degrading bacteria and fungi is important for understanding how microorganisms can be used to address the problem of plastic pollution and for developing new approaches to sustainable waste management and bioplastic production. In the present study, we isolated 55 bacterial and 184 fungal strains degrading polycaprolactone (PCL) in plastic waste samples from Dafeng coastal salt marshes, Jiangsu, China. Of these, Jonesia and Streptomyces bacteria also showed potential to degrade other types of petroleum-based polymers. The metabarcoding results proved the existence of plastisphere as a distinct ecological niche regardless of the plastic types where 27 bacterial and 29 fungal amplicon sequence variants (ASVs) were found to be significantly (p < 0.05) enriched, including some belonging to Alternaria (Ascomycota, Fungi) and Pseudomonas (Gammaproteobacteria, Bacteria) that were also mined out by the method of cultivation. Further assembly analyses demonstrated the importance of deterministic processes especially the environmental filtering effect of carbon content and pH on bacteria as well as the carbon and cation content on fungi in shaping the plastisphere communities in this ecosystem. Thus, the unique microbiome of the plastisphere in the terrestrial-marine ecotone is enriched with microorganisms that are potentially capable of utilizing petroleum-based polymers, making it a valuable resource for screening plastic biodegraders.
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Affiliation(s)
- Guan Pang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuesong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Mingyue Ding
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Siqi Jiang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Peijie Chen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Zheng Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Renwei Gao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Song
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, China
| | - Xiaowei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng M Cai
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China.
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Resendiz-Nava CN, Alonso-Onofre F, Silva-Rojas HV, Rebollar-Alviter A, Rivera-Pastrana DM, Stasiewicz MJ, Nava GM, Mercado-Silva EM. Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System. Microorganisms 2023; 11:1633. [PMID: 37512805 PMCID: PMC10383152 DOI: 10.3390/microorganisms11071633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.
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Affiliation(s)
- Carolina N Resendiz-Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | | | - Hilda V Silva-Rojas
- Posgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, Mexico
| | - Angel Rebollar-Alviter
- Centro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, Mexico
| | - Dulce M Rivera-Pastrana
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Gerardo M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Edmundo M Mercado-Silva
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
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20
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Li ZR, Luo SQ, Peng YJ, Jin CZ, Liu DC. Effect of long-term application of bioorganic fertilizer on the soil property and bacteria in rice paddy. AMB Express 2023; 13:60. [PMID: 37310515 DOI: 10.1186/s13568-023-01559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/14/2023] [Indexed: 06/14/2023] Open
Abstract
The application of novel bioorganic fertilizer (BIO) has been established as a weed biocontrol strategy, and reduce herbicides pollution and negatively effects on agricultural ecosystems. However, its long-term influences on soil bacterial communities are unknown. Here, 16 S rRNA sequencing to identify the changes that occur in soil bacterial community and enzyme under BIO treatments after five years in a field experiment. BIO application effectively controlled weeds, however no obvious differences between treatments were observed under BIO-50, BIO-100, BIO-200 and BIO-400 treatment. Anaeromyxobacter and Clostridium_ sensu_ stricto_1 were the two dominant genera among BIO-treated soil samples. The BIO-800 treatment had a slight influence on the species diversity index, which was more remarkable after five years. The seven significantly-different genera between BIO-800 treatment and untreated soils included C._sensu_stricto_1, Syntrophorhabdus, Candidatus_Koribacter, Rhodanobacter, Bryobacter, Haliangium, Anaeromyxobacter. In addition, BIO application had different effects on soil enzymatic activities and chemical properties. The extractable P and pH saliency correlated with Haliangium and C._Koribacter, and C._sensu_stricto_1 observably correlated with exchangeable K, hydrolytic N and organic matter. Taken together, our data suggest that BIO application effectively controlled weeds and a slight influence on soil bacterial communities and enzymes. These findings expand our knowledge of the application of BIO as widely used as a sustainable weed control in rice paddy.
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Affiliation(s)
- Zu-Ren Li
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China.
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Si-Quan Luo
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Ya-Jun Peng
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Chen-Zhong Jin
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Du-Cai Liu
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China.
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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21
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Hughes RL, Frankenfeld CL, Gohl DM, Huttenhower C, Jackson SA, Vandeputte D, Vogtmann E, Comstock SS, Kable ME. Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session [13 October 2022]. Nutrients 2023; 15:nu15112451. [PMID: 37299414 DOI: 10.3390/nu15112451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/14/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The microbial cells colonizing the human body form an ecosystem that is integral to the regulation and maintenance of human health. Elucidation of specific associations between the human microbiome and health outcomes is facilitating the development of microbiome-targeted recommendations and treatments (e.g., fecal microbiota transplant; pre-, pro-, and post-biotics) to help prevent and treat disease. However, the potential of such recommendations and treatments to improve human health has yet to be fully realized. Technological advances have led to the development and proliferation of a wide range of tools and methods to collect, store, sequence, and analyze microbiome samples. However, differences in methodology at each step in these analytic processes can lead to variability in results due to the unique biases and limitations of each component. This technical variability hampers the detection and validation of associations with small to medium effect sizes. Therefore, the American Society for Nutrition (ASN) Nutritional Microbiology Group Engaging Members (GEM), sponsored by the Institute for the Advancement of Food and Nutrition Sciences (IAFNS), hosted a satellite session on methods in nutrition and gut microbiome research to review currently available methods for microbiome research, best practices, as well as tools and standards to aid in comparability of methods and results. This manuscript summarizes the topics and research discussed at the session. Consideration of the guidelines and principles reviewed in this session will increase the accuracy, precision, and comparability of microbiome research and ultimately the understanding of the associations between the human microbiome and health.
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Affiliation(s)
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Curtis Huttenhower
- Department of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott A Jackson
- Complex Microbial Systems Group, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Doris Vandeputte
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah S Comstock
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI 48824, USA
| | - Mary E Kable
- USDA-ARS Western Human Nutrition Research Center, University of California-Davis, Davis, CA 95616, USA
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22
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Wang G, Zhang L, Guo Z, Shi D, Zhai H, Yao Y, Yang T, Xin S, Cui H, Li J, Ma J, Sun W. Benefits of biological nitrification inhibition of Leymus chinensis under alkaline stress: the regulatory function of ammonium-N exceeds its nutritional function. FRONTIERS IN PLANT SCIENCE 2023; 14:1145830. [PMID: 37255563 PMCID: PMC10225694 DOI: 10.3389/fpls.2023.1145830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023]
Abstract
Introduction The production of root exudates with biological nitrification inhibition (BNI) effects is a strategy adopted by ammonium-N (NH4+-N) tolerant plant species that occur in N-limited environments. Most knowledge on BNI comes from plant species that occur in acidic soils. Methods Here, combining field sampling and laboratory culture, we assessed the BNI-capacity of Leymus chinensis, a dominant grass species in alkaline grasslands in eastern Asia, and explored why L. chinensis has BNI ability. Results and discussion The results showed that L. chinensis has strong BNI-capacity. At a concentration of 1 mg mL-1, L. chinensis' root exudates inhibited nitrification in soils influenced by Puccinellia tenuiflora by 72.44%, while DCD only inhibited it by 68.29%. The nitrification potential of the soil of L. chinensis community was only 53% of the P. tenuiflora or 41% of the Suaeda salsa community. We also showed that the supply of NH4+-N driven by L. chinensis' BNI can meet its requirements . In addition, NH4+-N can enhance plant adaptation to alkaline stress by regulating pH, and in turn, the uptake of nitrate-N (NO3--N). We further demonstrated that the regulatory function of NH4+-N is greater than its nutritional function in alkaline environment. The results offer novel insights into how L. chinensis adapts to high pH and nutrient deficiency stress by secreting BNIs, and reveal, for the first time, differences in the functional roles of NH4+-N and NO3--N in growth and adaptation under alkaline conditions in a grass species.
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Affiliation(s)
- Gui Wang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
- School of Life Sciences, Changchun Normal University, Changchun, Jilin, China
| | - Lihui Zhang
- School of Life Sciences, Changchun Normal University, Changchun, Jilin, China
| | - Zihan Guo
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Dongfang Shi
- Analysis and Testing Center, Changchun Normal University, Changchun, Jilin, China
| | - Huiliang Zhai
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Yuan Yao
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Tianxue Yang
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Shuquan Xin
- School of Life Sciences, Changchun Normal University, Changchun, Jilin, China
| | - Haiying Cui
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Junqin Li
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
| | - Jianying Ma
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
| | - Wei Sun
- Institute of Grassland Science, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Northeast Normal University, Changchun, China
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23
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The Effect of Lactiplantibacillus plantarum ZZU203, Cellulase-Producing Bacillus methylotrophicus, and Their Combinations on Alfalfa Silage Quality and Bacterial Community. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
This study assessed the effects of Lactiplantibacillus plantarum (ZZU203), cellulase-producing Bacillus methylotrophicus (CB), or their combination (ZZU203_CB) on the fermentation parameters of alfalfa after 10 and 60 days of ensiling. Additionally, the bacterial community compositions were analyzed using absolute quantification 16S-seq (AQS). The results showed that CB silage displayed a higher lactic acid (LA) concentration at 10 d, a higher abundance of Lactobacillus, and lower abundance of Pediococcus, Enterococcus, and Weissella than those in the control (CK) silage. Compared with CK silage, the ZZU203 silage increased LA concentration, fructose and rhamnose concentrations, and the abundance of Lactobacillus, and decreased pH value, ammoniacal nitrogen, acetic acid, neutral detergent fiber and acid detergent fiber concentrations, and the abundance of Pediococcus, Enterococcus, Weissella, Hafnia, and Garciella after 60 days of ensiling. In addition, ZZU203 and ZZU203_CB silage had a similar silage quality and bacterial community, while the inoculation of ZZU203_CB significantly promoted LA accumulation and the numbers of Lactobacillus at 10 d compared with ZZU203 silage. Therefore, ZZU203 or a combination of ZZU203 and CB can be used as potential silage additives to improve the silage quality of alfalfa.
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Guan X, Cheng Z, Li Y, Wang J, Zhao R, Guo Z, Zhao T, Huang L, Qiu C, Shi W, Jin S. Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 330:117137. [PMID: 36584462 DOI: 10.1016/j.jenvman.2022.117137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Zhen Cheng
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Yiqiang Li
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, No. 17 Qinghuadong Road, Haidian District, Beijing, 100083, China.
| | - Ruoyu Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Zining Guo
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Tingting Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), Beijing, 100083, China
| | - Liying Huang
- Institute of Agricultural Quality Standards and Testing, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, 850031, China
| | - Cheng Qiu
- Institute of Agricultural Quality Standards and Testing, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, 850031, China
| | - Wenyu Shi
- College of Food Science & Nutritional Engineering, China Agricultural University, No. 17 Qinghuadong Road, Haidian District, Beijing, 100083, China
| | - Song Jin
- Department of Civil and Architectural Engineering, University of Wyoming, Laramie, WY, 82071, USA.
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Zhang Y, Cheng Z, Li Q, Dai Q, Hu J. Responses of rhizosphere bacterial communities in newly reclaimed mudflat paddies to rice genotype and nitrogen fertilizer rate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:38761-38774. [PMID: 36586025 DOI: 10.1007/s11356-022-25020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays a vital role in crop growth and adaptation. However, the effects of rice genotype, nitrogen (N) fertilization, and their interactions on the rhizosphere bacterial communities in low fertility soil remain poorly understood. In this study, a two-factor field experiment was performed in newly reclaimed mudflat paddies characterized by poor fertility to analyze bacterial communities in the rhizosphere of Yongyou 2640 (japonica/indica hybrid rice, JIH) and Huaidao No.5 (japonica conventional rice, JC) under different N fertilizer rates. Results showed that genotype, followed by N fertilizer rate, was the primary factor affecting rhizobacteria diversity. Rhizobacteria diversity was higher in JIH than in JC and that of JIH and JC did not significantly change overall as N fertilizer rates but increased and decreased at N fertilizer rates of over 300 kg N ha-1, respectively. The inconsistent response was probably attributed to the difference in the increase of ammonium and/or nitrate in the rhizosphere of JIH and JC. Genotype explained approximately 26% of the variation in rhizosphere bacterial communities. Rhizosphere bacterial communities with N fertilizer rates of over 300 kg N ha-1 were more dissimilar to those without N fertilization relative to those with N fertilizer rates of below 300 kg N ha-1, which was mainly attributed to changes in the concentration of ammonium and/or nitrate. The relative abundances of some potential beneficial genera such as Salinimicrobium, Salegentibacter, Gillisia, and Anaerolinea in the rhizosphere of JC and Salegentibacter, Lysobacter, Nocardioides, and Pontibacter in the rhizosphere of JIH were increased under N fertilizer rates of less than 300 kg N ha-1 and positively correlated with rice yields, which indicate that changes in bacterial communities caused by N fertilization might be strongly associated with the improvement of rice yield. Overall, rhizosphere bacterial communities were more sensitive to genotype in newly reclaimed mudflat paddies and showed a consistent response to N fertilizer rates.
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Affiliation(s)
- Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
| | - Zhandou Cheng
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou, 225127, China
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Lu C, Hou K, Zhou T, Wang X, Zhang J, Cheng C, Du Z, Li B, Wang J, Wang J, Zhu L. Characterization of the responses of soil micro-organisms to azoxystrobin and the residue dynamics of azoxystrobin in wheat-corn rotation fields over two years. CHEMOSPHERE 2023; 318:137918. [PMID: 36702407 DOI: 10.1016/j.chemosphere.2023.137918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/26/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Azoxystrobin, a high-efficiency and broad-spectrum strobilurin fungicide, has been widely used in global agricultural production. However, the effects of azoxystrobin on soil micro-organisms have scarcely been studied, and relevant experiments are usually conducted under laboratory conditions using active ingredient. Therefore, the effects of azoxystrobin on soil micro-organisms when applied to actual farmland are unknown. We sought to address this knowledge gap in this study, where we studied the effects of azoxystrobin on soil micro-organisms in a wheat-corn rotation field over two years. The results indicate that after two years of azoxystrobin application the activities of soil enzymes were inhibited, and the abundance of functional genes related to the nitrogen and carbon cycle were inhibited, which change the abundance of soil microbial bacteria of genera. As a consequence, the soil nitrogen and carbon cycles were disturbed. In addition, azoxystrobin inhibited the abundance of functional bacteria related to organic pollutant degradation and soil metabolism, where the rate of azoxystrobin degradation diminished over time. Moreover, azoxystrobin significantly inhibited the soil-culturable microbial population. The integrated biomarker response (IBR) indicated that the soil-culturable microbial population can be used as a sensitive indicator of the effect of azoxystrobin on soil micro-organisms. The final levels of azoxystrobin residues measured in grains were less than 0.004 mg/kg, lower than the maximum residue limits in European Union and China. The results of this study provide a basis for suggestions regarding the appropriate use of azoxystrobin in addition to support for elucidating the interaction between biological macromolecules and pollutants.
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Affiliation(s)
- Chengbo Lu
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Kaixuan Hou
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Tongtong Zhou
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Xiaole Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Jingwen Zhang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Chao Cheng
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
| | - Lusheng Zhu
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, Taian, 271018, PR China.
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Lei J, Wu H, Li X, Guo W, Duan A, Zhang J. Response of Rhizosphere Bacterial Communities to Near-Natural Forest Management and Tree Species within Chinese Fir Plantations. Microbiol Spectr 2023; 11:e0232822. [PMID: 36688690 PMCID: PMC9927156 DOI: 10.1128/spectrum.02328-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Near-natural forest management plays an important role in the maintenance of the long-term productivity and soil fertility of plantations. We conducted high-throughput absolute quantitative sequencing of 16S rRNA genes to compare the structures and diversity of rhizosphere soil bacterial communities among a pure Chinese fir (Cunninghamia lanceolata) plantation (S), a Cunninghamia lanceolata-Castanopsis hystrix-Michelia hedyosperma mixed plantation (SHX), and a Cunninghamia lanceolata-Castanopsis fissa mixed plantation (SD). The results revealed that near-natural forest management improved the rhizosphere soil properties of Chinese fir, especially the phosphorus content. Rhizosphere soil bacterial communities of Chinese fir in SHX and SD contained higher total absolute abundances and more unique operational taxonomic units (OTUs) than the pure plantation forest. Planctomycetes and Actinobacteria were abundant in SD, and Actinobacteria were enriched in SHX. The tree species also had an impact on the rhizosphere soil bacterial communities. For the rhizosphere soils of different tree species of SHX, the available phosphorus (AP) content of the rhizosphere of Chinese fir significantly surpassed those of Castanopsis hystrix and Michelia hedyosperma. Bacteria related to nitrogen fixing, such as Burkholderiales and Rhizobiales, were more abundant in Chinese fir in SD than in Castanopsis fissa. Acdiobacteria and Proteobacteria underpinned the differences found in the compositions of soil bacteria. The pH and soil organic matter were key variables influencing the rhizosphere soil bacterial communities. Our results demonstrated that in Chinese fir plantations, 12 years of near-natural management of introduced broad-leaved tree species can drive alterations of the physicochemical characteristics, bacterial community structure, and composition of rhizosphere soil, with tree species identity further influencing the rhizosphere soil bacterial community. IMPORTANCE Near-natural forest management is an important way to change the soil fertility decline and productivity reduction of pure Chinese fir plantations. At present, many detailed studies have been carried out on the impact of near-natural forest management on Chinese fir plantations at home and abroad. However, there are still few studies on the response of rhizosphere bacterial communities to near-natural forest management. Our study determined absolute quantities of Chinese fir rhizosphere bacterial communities in different mixed patterns. The results underscore the importance of near-natural forest management for Chinese fir plantation rhizosphere bacterial communities and provide new information on soil factors that affect rhizosphere bacterial communities in South China.
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Affiliation(s)
- Jie Lei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Hanbin Wu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Xiaoyan Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Wenfu Guo
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang, People's Republic of China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, People's Republic of China
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Yu Q, Han Q, Shi S, Sun X, Wang X, Wang S, Yang J, Su W, Nan Z, Li H. Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160324. [PMID: 36410491 DOI: 10.1016/j.scitotenv.2022.160324] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.
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Affiliation(s)
- Qiaoling Yu
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Shunqin Shi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaofang Sun
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhibiao Nan
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microiome, Lanzhou University, Lanzhou 730000, China; School of Public Health, Lanzhou University, Lanzhou 730000, China.
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Li X, Li D, Jiang Y, Xu J, Ren X, Zhang Y, Wang H, Lu Q, Yan J, Ahmed T, Li B, Guo K. The effects of microbial fertilizer based Aspergillus brunneoviolaceus HZ23 on pakchoi growth, soil properties, rhizosphere bacterial community structure, and metabolites in newly reclaimed land. Front Microbiol 2023; 14:1091380. [PMID: 36814570 PMCID: PMC9939755 DOI: 10.3389/fmicb.2023.1091380] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023] Open
Abstract
Introduction Pakchoi is an important leafy vegetable in China. Due to industrialization and urbanization, pakchoi has been cultivated in newly reclaimed mountainous lands in Zhejiang Province, China in recent years. However, immature soil is not suitable for plant growth and needs to be modified by the application of different organic fertilizer or microbial fertilizer based plant-growth-promoting microbe. In 2021, a high efficient plant-growth-promoting fungi (PGPF; Aspergillus brunneoviolaceus HZ23) was obtained from newly reclaimed land of Zhejiang Province, China. In order to valuate microbial fertilizer based A. brunneoviolaceus HZ23 (MF-HZ23) on pakchoi growth in immature soil, we investigated the effect of MF-HZ23 on soil properties, rhizosphere bacterial community structure, and metabolites of pakchoi rhizosphere soil samples. Methods The field experiment (four treatments, MF-HZ23, MF-ZH23 + CCF, CCF and the control) was completely randomly designed and carried out on newly reclaimed land in Yangqingmiao Village of Fuyang district, Hangzhou City, Zhejiang Province, China. In order to evaluate the influence of microbial fertilizer based A. brunneoviolaceus HZ23 on pakchoi in the newly reclaimed land, the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. In addition, the soil properties, including the pH, OMC, total N, AHN, available P, the genome sequencing, and metabolomics assay were also detected. Results The results revealed a significant difference between MF-HZ23 and the control in soil properties, bacterial community structure, and metabolites. Indeed, compared with the control, MF-HZ23 caused 30.66, 71.43, 47.31, 135.84, and 2099.90% increase in the soil pH, organic matter contents (OMC), total nitrogen (N), alkaline hydrolysis nitrogen (AHN), and available phosphorus (P), respectively. Meanwhile, MF-HZ23 caused 50.78, 317.47, and 34.40% increase in the relative abundance of Proteobacteria, Bacteroidota, and Verrucomicrobiota and 75.55, 23.27, 69.25, 45.88, 53.42, and 72.44% reduction in the relative abundance of Acidobacteriota, Actinobacteriota, Chloroflexi, Planctomycetota, Patescibacteria, and WPS-2, respectively, compared with the control based on 16S amplicon sequencing of soil bacteria. Furthermore, redundancy discriminant analysis (RDA) of bacterial communities and soil properties indicated that the main variables of bacterial communities included available P, AHN, pH, OMC, and total N. In addition, non-targeted metabolomics techniques (UHPLC-MS analysis) revealed that MF-HZ23 resulted in a great change in the kinds of metabolites in the rhizosphere soil. Indeed, in MF-HZ23 and the control group, there were six differentially expressed metabolites (DEMs) belong to organoheterocyclic compounds, organic acids and derivatives, organic nitrogen compounds, and these six DEMs were significantly positively correlated with 23 genus of bacteria, which showed complicated interactions between bacteria and DEMs in pakchoi rhizosphere soil. Conclutions Overall, the results of this study revealed significant modification in physical, chemical, and biological properties of pakchoi soil. Microbial fertilizer based PGPF A. brunneoviolaceus HZ23 (MF-HZ23) can be used as a good amendment for newly reclaimed land.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Dingyi Li
- Department of Biological Environment, Material and Environmental CollegeShanxi Jinzhong Institute of Technology, Jinzhong, China
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, China
| | - Jun Xu
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Ya Zhang
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Hong Wang
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiujun Lu
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou, China,*Correspondence: Qiujun Lu, ✉
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China,Jianli Yan, ✉
| | - Temoor Ahmed
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Guo
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China,Kai Guo, ✉
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30
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Wang J, Li M, Zhou Q, Zhang T. Effects of continuous cropping Jiashi muskmelon on rhizosphere microbial community. Front Microbiol 2023; 13:1086334. [PMID: 36699602 PMCID: PMC9868712 DOI: 10.3389/fmicb.2022.1086334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction The continuous cropping of crops can result in the deterioration of the soil environment and cause a decline in plant health and yield, which complicates agricultural production. However, the effects of continuous melon cropping on rhizospheric microbial communities remain poorly understood. Methods In this study, high-throughput absolute quantification 16S rRNA gene amplicon sequencing was employed to analyze the bacterial community structure of greenhouse rhizosphere soil from Jiashi muskmelon replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively). Results The results showed that long- term continuous cropping caused significant changes in soil physicochemical properties. The bacterial absolute abundances increased, but the bacterial community richness and diversity were significantly lost (p < 0.05). The composition of bacterial community was more similar after 2 and 3 years of continuous cropping. The longer the continuous cropping years were, the greater the shift in the bacterial diversity and abundance. Analysis of potential functional components revealed that different bacterial groups were enriched in different continuous cropping years. The significant reduction of the taxa associated with nitrate reduction may be responsible for the loss of soil nitrogen in continuous cropping soil. Discussion In summary, continuous cropping had a significant impact on the bacterial community structure of Jiashi muskmelon rhizospheric soil, and these results will provide a reference for soil management and scientific fertilization of melon and other crops under a continuous cropping regime.
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Affiliation(s)
- Jilian Wang
- Department of Biologic and Geographic Sciences, Kashi University, Kashi, China,Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi, China
| | - Mingyuan Li
- Department of Biologic and Geographic Sciences, Kashi University, Kashi, China,Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi, China,*Correspondence: Mingyuan Li,
| | - Qian Zhou
- Department of Biologic and Geographic Sciences, Kashi University, Kashi, China,Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi, China
| | - Tian Zhang
- Department of Biologic and Geographic Sciences, Kashi University, Kashi, China,Key Laboratory of Biological Resources and Ecology of Pamirs Plateau in Xinjiang Uygur Autonomous Region, Kashi, China
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Ma J, Niu A, Liao Z, Qin J, Xu S, Lin C. Factors affecting N 2O fluxes from heavy metal-contaminated mangrove soils in a subtropical estuary. MARINE POLLUTION BULLETIN 2023; 186:114425. [PMID: 36462424 DOI: 10.1016/j.marpolbul.2022.114425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
A 1-year field monitoring program was carried out to observe seasonal variation in N2O fluxes at two typical mangrove wetlands in a subtropical estuary. The soils in the island-type mangrove wetland had a higher level of heavy metal(loid) contamination and a lower level of salinity compared to the small bay-type mangrove wetland. While there was a high level of similarity in the seasonal variation pattern of N2O fluxes between the two investigated sites with both being significantly higher in summer than in other seasons, the average of N2O fluxes in the island-type mangrove wetland was 7.19 μg·m-2·h-1, which tended to be lower compared to the small bay-type mangrove wetland (15.63 μg·m-2·h-1). Overall, N2O flux was closely related to soil-borne heavy metal(loid)s, showing a trend to decrease with increasing concentration of these heavy metal(loid)s. The N2O fluxes increased with decreasing abundance of either denitrifiers or nitrifiers. But the opposite was observed for the anammox bacteria present in the soils. The anammox bacteria were more sensitive to heavy metal(loid) stress but more tolerated high salinity encountered in the investigated soils compared to the denitrifiers or nitrifiers. It appears that anammox reactions mediated by anammox bacteria played a key role in affecting the spatial variation in N2O fluxes from the mangrove soils in the study area. And an increased level of ammonium in soils tended to promote the activity of anammox bacteria and consequently enhanced N2O emission from the mangrove soils.
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Affiliation(s)
- Jiaojiao Ma
- School of Geography, South China Normal University, Guangzhou 510631, China; Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Anyi Niu
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Zhenni Liao
- School of Geography, South China Normal University, Guangzhou 510631, China
| | - Junhao Qin
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Songjun Xu
- School of Geography, South China Normal University, Guangzhou 510631, China.
| | - Chuxia Lin
- Faculty of Science, Engineering and Built Environment, Deakin University, Burwood, VIC 3125, Australia.
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Liu W, Qiu K, Xie Y, Huang Y, Wang R, Li H, Meng W, He Y, Li Y, Li H, Zhao P, Yang Y. High-Throughput Absolute Quantification Sequencing Reveals that a Combination of Leguminous Shrubs Is Effective in Driving Soil Bacterial Diversity During the Process of Desertification Reversal. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02151-0. [PMID: 36495359 DOI: 10.1007/s00248-022-02151-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Desertification leads to the extreme fragility of ecosystems and seriously threatens ecosystem functioning in desert areas. The planting of xerophytes, especially leguminous shrubs, is an effective and common means to reverse desertification. Soil microorganisms play a crucial role in nutrient cycling and energy flow in ecosystems. However, the effects of introducing leguminous shrubs on soil microbial diversity and the relevant mechanisms are not clear. Here, we employed the high-throughput absolute quantification 16S rRNA sequencing method to analyze the diversity of soil bacteria in sand-fixing areas of mixed shrublands with three combinations of shrubs, i.e., C. korshinskii × Corethrodendron scoparium (CaKCoS), C. korshinskii × Calligonum mongolicum (CaKCaM), and C. scoparium × C. mongolicum (CoSCaM), in the south of the Mu Us Sandy Land, China. This area suffered from moving dunes 20 years ago, but after introducing these shrubs to fix the dunes, the ecosystem was restored. Additionally, the effects of soil physicochemical properties on soil bacterial composition and diversity were analyzed with redundancy analysis (RDA) and structural equation modeling (SEM). It was found that the Shannon index of soil bacteria in CaKCoS was significantly higher than that in CaKCaM and CoSCaM, and the abundance of the dominant phyla, including Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Thaumarchaeota, Armatimonadetes, candidate_division_WPS-1, and Nitrospirae, increased significantly in CaKCoS and CaKCaM compared to that in CoSCaM. RDA showed that the majority of soil properties, such as total nitrogen (TN), available potassium (AK), N:P ratio, soil moisture (SM), and available phosphorus (AP), were important soil environmental factors affecting the abundance of the dominant phyla, and RDA1 and RDA2 accounted for 56.66% and 2.35% of the total variation, respectively. SEM showed that the soil bacterial α-diversity was positively affected by the soil organic carbon (SOC), N:P ratio, and total phosphorus (TP). Moreover, CaKCoS had higher SM, total carbon (TC), total potassium (TK), and AP than CaKCaM and CoSCaM. Collectively, these results highlight a conceptual framework in which the combination of leguminous shrubs can effectively drive soil bacterial diversity by improving soil physicochemical properties and maintaining ecosystem functioning during desertification reversal.
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Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, 750199, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China.
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, 750021, Ningxia, China.
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, 750021, Ningxia, China.
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
- Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, 750021, Ningxia, China
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, 750021, Ningxia, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Lingwu, 750400, Ningxia, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Lingwu, 750400, Ningxia, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Haiquan Li
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Pengbo Zhao
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
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Lin X, Li Y, Xu G, Tian C, Yu Y. Biodegradable microplastics impact the uptake of Cd in rice: The roles of niche breadth and assembly process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158222. [PMID: 36028027 DOI: 10.1016/j.scitotenv.2022.158222] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Biodegradable microplastics (MPs) can impact the accumulation of cadmium (Cd) by plants, however, its mechanisms have not been fully understood. In this study, two biodegradable MPs, polypropylene carbonate (PPC) and polylactic acid (PLA), were used to examine their influences on the uptake of Cd in rice plants. Results showed that PPC significantly reduced the accumulation of Cd in rice root and aerial part, whereas PLA increased the Cd concentrations in rice root. The random forest analysis revealed that the bacterial biomarkers enriched by two MPs were different at genus level. Niche breadths were significantly reduced under Cd stress, and PPC alleviated this environmental pressure for entire bacterial community, whereas PLA reduced the niche breadth for whole community and abundant taxa, which was further verified by co-occurrence network and normalized stochasticity ratio model. The abundant taxa of group PPC were primarily governed by deterministic process while rare taxa were more driven by stochastic process. Structural equation model and Mantel analysis identified that the niche breadth imposed a strong selection on Cd accumulation after co-exposure. This study reveals the underlying mechanism of assembly process and niche breadth of rice rhizosphere microbiome on Cd accumulation by rice plants.
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Affiliation(s)
- Xiaolong Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjun Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guanghui Xu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Chunjie Tian
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Yao Z, Zhu Y, Wu Q, Xu Y. Challenges and perspectives of quantitative microbiome profiling in food fermentations. Crit Rev Food Sci Nutr 2022; 64:4995-5015. [PMID: 36412251 DOI: 10.1080/10408398.2022.2147899] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.
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Affiliation(s)
- Zhihao Yao
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Zhu
- Bioprocess Engineering, Wageningen University and Research, Wageningen, The Netherlands
| | - Qun Wu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, The Key Laboratory of Industrial Biotechnology, Ministry of Education; State Key Laboratory of Food Science and Technology; School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Li Y, Zhu F, Li Y, Pan S, Wang H, Yang Z, Wang Z, Hu Z, Yu J, Barritt JD, Li T, Liu X, Wang Y, Ma X, Liu B. Bacteriophages allow selective depletion of gut bacteria to produce a targeted-bacterium-depleted mouse model. CELL REPORTS METHODS 2022; 2:100324. [PMID: 36452872 PMCID: PMC9701607 DOI: 10.1016/j.crmeth.2022.100324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/11/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
The gut microbiome is essential for human health. Mouse microbiota models, including gnotobiotic mice, are the most prominent tools to elucidate the functions of gut bacteria. Here, we propose a targeted-bacterium-depleted (TBD) model using lytic bacteriophage to selectively deplete gut bacterium of healthy or otherwise defined mice. These phage-treated animals should have a near-complete spectrum of gut bacteria except for the depleted bacterium. To prove the concept, we employed Escherichia coli-specific phage T7 to repress E. coli in the healthy mice. Our results showed that the E. coli-depleted mice exhibited bravery-like behaviors, correlated to the presence of E. coli rather than the equilibrium among gut bacteria. Thus, we demonstrate that the TBD model is a powerful tool to elucidate the function of a specific bacterial species within a near-intact gut microbiota environment and complements gnotobiotic mice models.
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Affiliation(s)
- Yanqing Li
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Feng Zhu
- Department of Psychiatry, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
- Center for Brain Research, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Yan Li
- Center for Brain Research, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Shunli Pan
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Hongliang Wang
- Department of Pathogen Biology and Immunology, Xi’an Jiaotong University Health Science Center, Xi’an, Shaanxi 710061, China
| | - Zai Yang
- Department of Psychiatry, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Zhihao Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Zhenyu Hu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Jianfeng Yu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Joseph D. Barritt
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tianhui Li
- Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Xi Liu
- Department of Pathology, First Affiliated Hospital of Xi’ an Jiaotong University, Xi’an, Shaanxi 710061, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Xiancang Ma
- Department of Psychiatry, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
- Center for Brain Research, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi 710061, China
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Wang T, Cheng K, Huo X, Meng P, Cai Z, Wang Z, Zhou J. Bioorganic fertilizer promotes pakchoi growth and shapes the soil microbial structure. FRONTIERS IN PLANT SCIENCE 2022; 13:1040437. [PMID: 36426155 PMCID: PMC9679507 DOI: 10.3389/fpls.2022.1040437] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
As a functional probiotic, Bacillus subtilis can promote crop growth and improve nutrient utilization by various mechanisms, so it has been made into bioorganic fertilizer as a replacement for chemical fertilizer. However, the effects of B. subtilis bioorganic fertilizer application on the yield and quality of commercial crops of Brassica chinensis L., the soil physicochemical properties and the microflora have not been clarified. In this study, pot experiments were conducted using Brassica chinensis L. plants with four fertilization treatments: control without fertilization (CK), chemical fertilizer (CF), organic fertilizer (OF), and bioorganic fertilizer containing B. subtilis (BF). After 30 days of pot experiment, the results showed that BF efficiently improved plant height and biomass (1.20- and 1.93-fold, respectively); as well as significantly increasing soil available potassium and pH value. Using high-throughput sequencing, we examined the bacterial and fungal communities in the soil, and found that their diversity was remarkablely reduced in the BF treatment compared to CK group. A principal coordinate analysis also showed a clear separation of bacterial and fungal communities in the BF and CK groups. After application of B. subtilis bioorganic fertilizer, some beneficial bacteria (such as Bacillus and Ammoniphilus) and fungi (Trichoderma and Mortierella) were enriched. A network analysis indicated that bacteria were the dominant soil microbes and the presence of B. subtilis stimulated the colonization of beneficial microbial communities. In addition, predictive functional profiling demonstrated that the application of bioorganic fertilizer enhanced the function of mineral element metabolism and absorption and increased the relative abundance of saprotrophs. Overall, the application of bioorganic fertilizer effectively changed the soil microflora, improved the soil available potassium and pH value, and boosted the yield of Brassica chinensis L. This work has valuable implications for promoting the safe planting of facility vegetables and the sustainable development of green agriculture.
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Affiliation(s)
- Tao Wang
- Institute of Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Keke Cheng
- Institute of Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xingjuan Huo
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, China
| | - Pinpin Meng
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, China
| | - Zhonghua Cai
- Institute of Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zongkang Wang
- Ecological Fertilizer Research Institute, Shenzhen Batian Ecological Engineering Co., Ltd., Shenzhen, China
| | - Jin Zhou
- Institute of Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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Liu W, Qiu K, Xie Y, Wang R, Li H, Meng W, Yang Y, Huang Y, Li Y, He Y. Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N. PeerJ 2022; 10:e14271. [PMID: 36340191 PMCID: PMC9635361 DOI: 10.7717/peerj.14271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.
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Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, China,Department of Desertification Prevention, Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, China
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Li Q, Zhang Y, Hu J, Dai Q. Response of bacterial communities and nitrogen-cycling genes in newly reclaimed mudflat paddy soils to nitrogen fertilizer gradients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:71113-71123. [PMID: 35595885 DOI: 10.1007/s11356-022-20770-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Conversion of coastal mudflats into paddy soils is an effective measure to alleviate the pressures on land resources. However, few studies have evaluated the effects of nitrogen (N) fertilizers on bacterial communities in newly reclaimed mudflat paddy soils. We performed a field plot experiment with six N fertilizer rates (0, 210, 255, 300, 345, and 390 kg N ha-1) in a newly reclaimed mudflat paddy for 2 consecutive years and used Illumina sequencing and qPCR to investigate the effects of N fertilizers on bacterial communities and N-cycling genes. Results showed that high N fertilization (above 300 kg N ha-1) increased the contents of organic matter (OM), total N (TN), ammonium (NH4+), and nitrate (NO3-) and significantly decreased the diversity and richness of bacteria. Furthermore, high N fertilization had a stronger effect on bacterial communities than low N fertilization, probably due to high concentrations of NH4+, OM, and NO3-. Additionally, in paddy soils with high N fertilizer application, the relative abundances of Bacteroidetes, γ-proteobacteria, and Actinobacteria increased significantly, but the reverse was true for those of Chloroflexi, Firmicutes, δ-proteobacteria, α-proteobacteria, Acidobacteria, and β-proteobacteria. The results of qPCR indicated that high N fertilization significantly increased the relative abundance of nifH genes involved in N fixation and decreased that of amoA-archaea involved in ammonia oxidation, nirS genes involved in nitrite reduction, and nosZ genes involved in nitrous oxide reduction, which suggested that high N fertilization increased the potential of available N retention and reduced the potential of nitrous oxide emission. Overall, N fertilizers with an N fertilizer rate of above 300 kg N ha-1 significantly altered the bacterial communities and N-cycle of mudflat paddy soils.
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Affiliation(s)
- Qing Li
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yang Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Jian Hu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetic and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Meng L, Pan S, Zhou L, Santasup C, Su M, Tian D, Li Z. Evaluating the survival of Aspergillus niger in a highly polluted red soil with addition of Phosphogypsum and bioorganic fertilizer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:76446-76455. [PMID: 35670942 DOI: 10.1007/s11356-022-21243-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Phosphate-solubilizing fungi (PSF) can enhance P release from phosphate minerals to immobilize heavy metals. However, this promotion substantially depends on their survival in highly polluted soils. The aim of this study was to investigate the survival of PSF after addition of phosphogypsum (PG) and bioorganic fertilizer (BF) in the soil with coexistence of multiple heavy metals, e.g., Pb, As, Cd, Sb, etc. Addition of typical PSF (Aspergillus niger) did not promote the formation of pyromorphite (the most stable form of Pb), possibly due to the buffering effect of the soil (the secreted oxalic acid was neutralized) and limited P supply. Meanwhile, despite that A. niger has high tolerance to heavy metal stress, its survival was significantly declined due to the deficiency of available P. It was also shown that PG, as the major by-product in phoschemical industry, still has relatively high available P compared with common natural soils. PG addition dramatically increased available P (up to 93.87 mg/kg) and the subsequent fungal growth. However, sole PG did not promote the formation of pyromorphite, probably as the abundant Fe2+ and Mn2+ prevented the contact between PO43- and Pb2+ in the soil system. The enhanced soil respiration after addition of BF and PG confirmed the promoted microbial activity (elevated to 3465.58 μg C kg h-1). This study showed PG's potential as P source for both microbial growth and heavy metal remediation in soil system. A combination of PG, A. niger, and BF can hence achieve long-term bioremediation of heavy metals.
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Affiliation(s)
- Lingzi Meng
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shang Pan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Limin Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Choochad Santasup
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Mu Su
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Da Tian
- Research Centre of Phosphorus Efficient Utilization and Water Environment Protection Along the Yangtze River Economic Belt, Anhui Agricultural University, Hefei, 230036, China
- Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, Key Laboratory of JiangHuai Arable Land Resources Protection and Eco-Restoration, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
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Li X, Lu Q, Li D, Wang D, Ren X, Yan J, Ahmed T, Li B. Effects of Two Kinds of Commercial Organic Fertilizers on Growth and Rhizosphere Soil Properties of Corn on New Reclamation Land. PLANTS (BASEL, SWITZERLAND) 2022; 11:2553. [PMID: 36235419 PMCID: PMC9571666 DOI: 10.3390/plants11192553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022]
Abstract
Due to the development of urbanization and industrialization, a large amount of cultivated land resources has been occupied, while new reclamation land could expand the supply of usable land for food security. Organic fertilizers, such as crop residues, biosolids, sheep manure, mushroom residue, and biogas liquid, have been considered as an effective amendment in immature soil to improve its quality. Recently, two kinds of commercial organic fertilizers, pig manure and mushroom residue organic fertilizer (PMMR-OF), and sheep manure organic fertilizer (SM-OF), have been more regularly applied in agriculture production. However, the information available on effect of the two kinds of fertilizers on plant growth and rhizosphere soil properties in immature field is very limited. In order to evaluate PMMR-OF and SM-OF on immature soil, the soil quality and microbial community structure of corn rhizosphere soil samples under the two kinds of organic fertilizers at different concentrations was investigated. The results revealed a significant difference between commercial organic fertilizers (especially SM-OF) and chemical compound fertilizers (CCF) in soil properties and microbial community structure. Indeed, compared with the control based on16S and ITS amplicon sequencing of soil microflora, SM-OF caused a 10.79-19.52%, 4.33-4.39%,and 14.58-29.29% increase in Proteobacteria, Actinobacteria, and Ascomycota, but a 5.82-20.58%, 0.53-24.06%, 10.87-16.79%, 2.69-10.50%, 44.90-59.24%, 8.88-10.98%, and 2.31-21.98% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Mortierellomycota, and Chytridiomycota, respectively. CCF caused a 24.11%, 23.28%, 38.87%, 19.88%, 18.28%, and 13.89% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Chytridiomycota, but a 22.77%, 41.28%, 7.88%, and 19.39% increase in Proteobacteria, Actinobacteria, Ascomycota, and Mortierellomycota, respectively. Furthermore, redundancy discriminant analysis of microbial communities and soil properties of PMMR-OF, SM-OF, CCF, and the control treatments indicated that the main variables of bacterial and fungal communities included organic matter content, available P, and available K. Overall, the results of this study revealed significant changes under different fertilizer conditions (PMMR-OF, SM-OF, CCF, under different concentrations) in microbiota and chemical properties of corn soil. Commercial organic fertilizers, particularly SM-OF, can be used as a good amendment for the new reclamation land.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Qiujun Lu
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou 310020, China
| | - Dingyi Li
- Department of Biological Environment, Material and Environmental College, Shanxi Jinzhong Institute of Technology, Jinzhong 030600, China
| | - Daoze Wang
- Rural Vitalization Service Center of Hangzhou, Hangzhou 310020, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China
| | - Temoor Ahmed
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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Cheng X, Tuoheti A, Huang X, Gu X. High-Throughput Sequencing Investigation of Bacterial Diversity in Chronic Suppurative Otitis Media and Middle Ear Cholesteatoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:9616582. [PMID: 36193141 PMCID: PMC9526669 DOI: 10.1155/2022/9616582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/31/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Background Chronic otitis media is a common middle ear disease in otolaryngology. Bacterial infection is considered as the cause of the disease, but relying on conventional bacterial cultures can be problematic for identifying specific pathogens. Current research suggests that bacteria in microbial communities can only be identified by rDNA sequencing of bacteria. Methods This cross-sectional study utilized broad-range PCR amplification of 16S rRNA genes with clone analysis to compare bacterial diversity in lesions from 6 patients with chronic suppurative otitis media (CSOM) and 10 patients with cholesteatoma of middle ear lesions. Bacteria were analyzed at the levels of phylum, order, family, genus, and species. Results The age and sex difference between the patients with chronic suppurative otitis media and the patients with middle ear cholesteatoma were comparable (P > 0.05). Bacterial species abundance and species diversity were greater in cholesteatoma of the middle ear lesions than in CSOM lesions. The total number of detected operational taxonomic units (OTU) was 838, comprising 788 OTU detected in cholesteatoma pathological tissues, 230 in CSOM pathological tissues, and 180 OTU common to both groups. Proteus is a major part of CSOM (99.46%, P = 0.000321). The phyla detected in the Cholesteatoma samples were Proteus (Proteobacteria) (35.77%), thikum (Firmicutes) (44.21%, P = 0.001071), and Actinomycetes (Actinobacteria) (16.66%, P = 0.032464). At all bacterial taxonomic levels, the epithelial tissue of middle ear cholesteatoma was complex in terms of bacterial diversity, covering many Gram-positive and Gram-negative bacteria, likely related to bacterial microbiome formation. In contrast, the bacteriology of the CSOM lesions was relatively simple at all taxonomic levels, with all sequences characterized as belonging to Gram-negative bacteria. Conclusion Our results suggest that persistent middle ear cholesteatoma infection may be a microbial flora disorder related to conditional pathogenic bacteria rather than a single bacterial infectious disease. The pathogen is relatively single in the diseased tissue of chronic suppurative otitis media, which is the main reason for its effective antiinfection treatment.
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Affiliation(s)
- Xiuqin Cheng
- Diagnosis and Treatment Center of Otorhinolaryngology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Abulajiang Tuoheti
- Diagnosis and Treatment Center of Otorhinolaryngology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Xiaobang Huang
- Department of Otorhinolaryngology Head and Neck Surgery, Tianjin Beichen Hospital, Tianjin, China
| | - Xingzhi Gu
- Otorhinolaryngology & Head and Neck Surgery, Sanya Central Hospital (Hainan Third People's Hospital), Sanya, Hainan, China
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Kang J, Chen X, Han BZ, Xue Y. Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu. Food Res Int 2022; 158:111488. [DOI: 10.1016/j.foodres.2022.111488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 11/25/2022]
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Li X, Lu Q, Li D, Wang D, Ren X, Yan J, Ahmed T, Li B. Effects of Different Microbial Fertilizers on Growth and Rhizosphere Soil Properties of Corn in Newly Reclaimed Land. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151978. [PMID: 35956458 PMCID: PMC9370191 DOI: 10.3390/plants11151978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 05/27/2023]
Abstract
Land reclamation may expand the supply of usable land for food security. Soil microorganisms have been considered as an amendment in immature soil to improve its quality. However, different microbial fertilizers' effects on plant growth in immature soil have largely been unexplored. In order to evaluate the effects of different microbial fertilizers on immature soil, the soil quality and microbial community structure of corn rhizosphere soil samples under different microbial fertilizers were investigated. The results revealed a significant difference between microbial fertilizers (especially seaweed microbial fertilizer, SMF) and commercial chemical compound fertilizers in the soil properties and microbial community structure. Indeed, SMF caused a 486.21%, 23.17%, 21.08%, 38.33%, and 482.39% increase in Flavobacteriaceae, Planctomycetaceae, Chitinophagaceae, Acidobacteria_Gp3, and Mortierellaceae but a 23.82%, 18.66%, 42.36%, 29.12%, 81.97%, 42.19%, and 99.33% reduction in Cytophagales, Comamonadaceae, Rhodospirillaceae, Sinobacteaceae, Aspergillaceae, Myrmecridiaceae, and Typhulaceae, respectively; while CCF caused an 85.68% and 183.22% increase in Xanthomonadaceae and Mortierellaceae but a 31.29%, 36.02%, and 65.74% reduction in Cytophagales, Spartobacteria, and Cyphellophoraceae compared with the control based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of the microbial communities and soil properties indicated that the main variables of the bacterial and fungal communities included exchangeable Ca, organic matter content, total N, and available P. Overall, the results of this study revealed significant changes under different fertilizer conditions in the microbiota and chemical properties of corn soil. Microbial fertilizers, particularly SMF and SM, can be used as a good amendment for newly reclaimed land.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; (X.L.); (X.R.)
| | - Qiujun Lu
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou 310020, China
| | - Dingyi Li
- Department of Biological Environment, Material and Environmental College, Shanxi Jinzhong Institute of Technology, Jinzhong 030600, China;
| | - Daoze Wang
- Rural Vitalization Service Center of Hangzhou, Hangzhou 310020, China;
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; (X.L.); (X.R.)
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China; (X.L.); (X.R.)
| | - Temoor Ahmed
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.A.); (B.L.)
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.A.); (B.L.)
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Xiao X, Li J, Lyu J, Feng Z, Zhang G, Yang H, Gao C, Jin L, Yu J. Chemical fertilizer reduction combined with bio-organic fertilizers increases cauliflower yield via regulation of soil biochemical properties and bacterial communities in Northwest China. Front Microbiol 2022; 13:922149. [PMID: 35966650 PMCID: PMC9363920 DOI: 10.3389/fmicb.2022.922149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/08/2022] [Indexed: 12/03/2022] Open
Abstract
The continuous application of chemical fertilizers in vegetable cropping has led to deterioration of the soil environment and reduced yield and quality. The objective of this study was to evaluate the effect of combining chemical and bio-organic fertilizers on cauliflower yield, soil biochemical properties, and the bacterial community. Six treatments were established: no fertilizer (CK, control), chemical fertilizers (CF, conventional dosage for this region), balanced fertilization (BF, 30% reduction of chemical fertilizers), and balanced fertilization plus 3,000, 6,000, or 12,000 kg.ha-1 bio-organic fertilizer (Lvneng Ruiqi Biotechnology Co., Ltd., Gansu, China) (BF + OF1, BF + OF2, BF + OF3, respectively). A two-season field experiment with cauliflower was conducted under the different fertilizer treatments in irrigation districts along the Yellow River, Northwest China. The results indicate that the yield, soil organic matter, total potassium content, and enzyme activity under the bio-organic treatments were generally higher than those under the CF treatment. Compared with the CF treatment, the BF treatment increased soil organic matter content, enzyme activity and soil bacterial relative abundance. Moreover, the bacterial alpha-diversity were higher than those of conventional fertilization. The predominant phyla, including Proteobacteria, Actinobacteria, Gemmatimonadetes, and Chloroflexi, were the main contributors to the microbiome shift, as demonstrated by their remarkable enrichment in the soil under BF + OF2 and BF + OF3 treatments. Furthermore, Pearson correlation analyses show significant correlations among the soil organic matter, available P and K, electrical conductivity, and relative abundance of potentially beneficial microbial groups, such as the genera Massilia, Bacillus, Lysobacter, and Nitrosospira. Overall, this study suggests that balanced fertilization and the application of bio-organic fertilizers are essential to ensure soil fertility and long-term sustainable green productivity.
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Affiliation(s)
- Xuemei Xiao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ju Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhi Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Guobin Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Haixing Yang
- Agricultural Technology Extension Center of Yuzhong County, Lanzhou, China
| | - Chengfei Gao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Li Jin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
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A High-Throughput Absolute Abundance Quantification Method for the Characterisation of Daqu Core Fungal Communities. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
An inherent issue in high-throughput sequencing applications is that they provide compositional data for relative abundance. This often obscures the true biomass and potential functions of fungi in the community. Therefore, we presented a high-throughput absolute quantification (HAQ) method to quantitatively estimate the fungal abundance in Daqu. In this study, five internal standard plasmids (ISPs) were designed for the fungal ITS2 subregion with high length variations. Five ISPs were then utilised to establish standard curves with a quantitative concentration range of 103–107 cells/g, and this was used to quantify the core fungi, including Basidiomycota, Ascomycota, and Mucoromycota. Using three types of mature Daqu from different regions, we demonstrated that the HAQ method yielded community profiles substantially different from those derived using relative abundances. Then, the HAQ method was applied to the Daqu during fermentation. The initial formation of the Daqu surface occurred in the fourth stage, which was mainly driven by moisture. The key fungi that caused the initial formation of the Daqu surface included Hyphopichia burtonii, Saccharomycopsis fibuligera, and Pichia kudriavzevii. The initial formation of the Daqu core occurred in the fifth stage, which was mainly affected by moisture and reducing the sugar content. The key fungi that cause the initial formation of the Daqu core included S. fibuligera and Paecilomyces verrucosus. We conclude that the HAQ method, when applied to ITS2 gene fungal community profiling, is quantitative and that its use will greatly improve our understanding of the fungal ecosystem in Daqu.
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Song X, Li H, Song J, Chen W, Shi L. Biochar/vermicompost promotes Hybrid Pennisetum plant growth and soil enzyme activity in saline soils. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:96-110. [PMID: 35576892 DOI: 10.1016/j.plaphy.2022.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/23/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Soil salinity has become a major threat to land degradation worldwide. The application of organic amendments is a promising alternative to restore salt-degraded soils and alleviate the deleterious effects of soil salt ions on crop growth and productivity. The aim of present study was to explore the potential impact of biochar and vermicompost, applied individually or in combination, on soil enzyme activity and the growth, yield and quality of Hybrid Pennisetum plants suffered moderate salt stress (5.0 g kg-1 NaCl in the soil). Our results showed that biochar and/or vermicompost promoted Na+ exclusion and K+ accumulation, relieved stomatal limitation, increased leaf pigment contents, enhanced electron transport efficiency and net photosynthesis, improved root activity, and minimized the oxidative damage in Hybrid Pennisetum caused by soil salinity stress. In addition, soil enzymes were also activated by biochar and vermicompost. These amendments increased the biomass and crude protein content, and decreased the acid detergent fiber and neutral detergent fiber contents in salt-stressed Hybrid Pennisetum. Biochar and vermicompost addition increased the biomass and quality of Hybrid Pennisetum due to the direct effects related to plant growth parameters and the indirect effects via soil enzyme activity. Finally, among the different treatments, the use of vermicompost showed better results than biochar alone or the biochar-compost combination did, suggesting that the addition of vermicompost to the soil is an effective and valuable method for reclamation of salt-affected soils.
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Affiliation(s)
- Xiliang Song
- College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Haibin Li
- College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Jiaxuan Song
- College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China
| | - Weifeng Chen
- College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
| | - Lianhui Shi
- College of Resources and Environment, Shandong Agricultural University, Tai'an, 271018, People's Republic of China.
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Liang D, Zhang X, Liu Z, Zheng R, Zhang L, Yu D, Shen X. The Genus Parabacteroides Is a Potential Contributor to the Beneficial Effects of Truncal Vagotomy-Related Bariatric Surgery. Obes Surg 2022; 32:1-11. [PMID: 35546385 PMCID: PMC9276728 DOI: 10.1007/s11695-022-06017-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/22/2022]
Abstract
PURPOSE Evidences about the gut microbiota role in weight loss after bariatric surgery (BS) are growing. The objective of this study was to observe the changes of gut microbiota after sleeve gastrectomy (SG) and SG plus truncal vagotomy (SG-TV) and identify specific microbes that may contribute to the improvement of obesity after surgeries. MATERIALS AND METHODS Forty high-fat diet-induced obesity (DIO) mice were randomized to SG, SG-TV, or sham operation (SH) groups. Body weight (BW) and fast blood glucose (FBG) were measured before and 1, 2, 4, 8, and 12 weeks post-operatively. Fecal samples were collected before and at post-operative week 12 and profiled using 16S rRNA relative and absolute quantitative sequencing. RESULTS After the surgery, the SG and SG-TV surgeries significantly reduce BW and FBG levels compared with SH, and the SG-TV achieved better effects than SG. A decreasing trend in alpha diversity of gut microbiota and significant changes in taxonomic composition were observed after surgeries. Then, we identified a set of microbes and pathways significantly different in abundance after BS. The genus Parabacteroides and one pathway (polyketide sugar unit biosynthesis) increased in SG-TV group specially, which was also negatively correlated with BW and FBG. CONCLUSION SG and SG-TV indeed achieve effects of weight loss, but TV could enhance the efficacy of SG. The identified different microbes and pathways, like Parabacteroides, polyketide sugar unit biosynthesis, may partly mediate the beneficial effects of BS, and thus possibly contribute to the development of novel bacteria-based therapeutic approaches.
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Affiliation(s)
- Dong Liang
- Translational Medicine Research Center, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Xin Zhang
- Department of General Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Zhaorui Liu
- Department of General Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Rui Zheng
- Department of General Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Longjiang Zhang
- Department of General Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, 200433, People's Republic of China
| | - Dong Yu
- Translational Medicine Research Center, Naval Medical University, Shanghai, 200433, People's Republic of China.
| | - Xiaojun Shen
- Department of General Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, 200433, People's Republic of China.
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Xiang F, Sheng J, Li G, Ma J, Wang X, Jiang C, Zhang Z. Black soldier fly larvae vermicompost alters soil biochemistry and bacterial community composition. Appl Microbiol Biotechnol 2022; 106:4315-4328. [PMID: 35595931 DOI: 10.1007/s00253-022-11947-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 11/02/2022]
Abstract
Black soldier fly larvae (Hermetia illucens L. BSFL) bioconversion is a promising biotechnology for food waste recycling, yet little is known about how BSFL vermicompost affects soil health in terms of element availability and related microbial response. In this work, a field soil experiment for luffa (Luffa cylindrica (L.) Roem.) growth was conducted to examine the impacts of BSFL vermicompost (BV, 9750 kg ha-1, equal to total N input rate of chemically treated soil (CK)) on soil biochemistry and bacterial communities. Relative to CK, application of BV significantly increased total soil carbon by 149% and enhanced catalase and urease activity by 59.2% and 16.2%, respectively. BV increased the degree of aromaticity and humification in dissolved organic matter (DOM) in soil by 28.6% and 27.3%, respectively, compared to CK treatment. Among bacterial communities in soil, Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria were the phyla that showed the most substantial alteration in response to BV. Redundancy analysis further revealed that the bacterial community structure was affected by DOM and total phosphorus. Functional analyses indicated that BV enhanced xylanolysis (55.4%) and nitrogen fixation (46.3%), but inhibited nitrification (59.8%). BSFL vermicompost input might effectively prevent the harm of soil borne pathogens (e.g., wilt). Moreover, these function groups strongly correlated with Clostridiales, Actinomycetales, and Nitrospirales. Our study reveals that BSFL vermicompost promoted soil nutrient availability, microbial community succession, and biochemical function optimization, which is conducive to the popularization and application of BSFL vermicompost in the field of soil health. KEY POINTS: • Vermicompost enhanced catalase and urease levels while increased DOM aromaticity. • Vermicompost enriched Bacteroidetes and Firmicutes and improved soil health.
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Affiliation(s)
- FangMing Xiang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China
| | - JianLin Sheng
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - Gang Li
- Yangtze Delta Region Healthy Agriculture Institute, TongXiang Economic HiTech Zone, Building 12#, Development Ave 133, TongXiang, 314515, People's Republic of China
| | - JingJin Ma
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China.,HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China
| | - XianZhe Wang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - ChengLiang Jiang
- HangZhou GuSheng Technology Company Limited, XiangWang Ave 311118, HangZhou, 311121, People's Republic of China.,ZheJiang FuMei Biotechnology Company Limited, PingYao Future Complex Park, PingYao Ave, HangZhou, 311115, People's Republic of China
| | - ZhiJian Zhang
- College of Natural Research and Environmental Sciences, ZheJiang University, YuHangTang Ave 688ZheJiang Province, HangZhou, 310058, People's Republic of China. .,China Academy of West Region Development, ZheJiang University, YuHangTang Ave 866, HangZhou, 310058, People's Republic of China.
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49
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Song Z, Sun Y, Liu P, Wang Y, Huang Y, Gao Y, Hu X. Invasion of
Spartina alterniflora
on
Zostera japonica
enhances the abundances of bacteria by absolute quantification sequencing analysis. Ecol Evol 2022; 12:e8939. [PMID: 35600690 PMCID: PMC9120208 DOI: 10.1002/ece3.8939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 04/15/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.
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Affiliation(s)
- Zenglei Song
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yanyu Sun
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Pengyuan Liu
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yibo Wang
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yanyan Huang
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Yan Gao
- Marine Science Research Institute of Shandong Province National Oceanographic Center of Qingdao Qingdao China
| | - Xiaoke Hu
- Key laboratory of Coastal Biology and Bioresource Utilization Yantai Institute of Costal Zone Research Chinese Academy of Sciences Yantai China
- Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao China
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50
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Li M, Zeng Z, Feng H, Cao Y, Zhang Q, Lv T, Yang X, Song D, Li P, Hu L, Fan S, An R, Zhang B, Zhang L, Liao Q. Accurate 16S Absolute Quantification Sequencing Revealed Vaginal Microecological Composition and Dynamics During Mixed Vaginitis Treatment With Fufang FuRong Effervescent Suppository. Front Cell Infect Microbiol 2022; 12:883798. [PMID: 35646743 PMCID: PMC9136393 DOI: 10.3389/fcimb.2022.883798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background The diagnosis and treatment of mixed vaginitis are more complicated than single pathogenic infections, and there may be adverse reactions and several contraindications to conventional antibiotic therapy. Therefore, this study aimed to evaluate the preliminary effects of Fufang Furong Effervescent Suppository for the management of aerobic vaginitis (AV) mixed with bacterial vaginosis (BV) using Accurate 16S absolute quantification sequencing (Accu16S). Methods In the present randomized, blind, multi-center clinical trial, women (20 to 55 years) who had received a diagnosis of AV+BV were randomly assigned into clindamycin positive control (n = 41) and Fufang Furong Effervescent Suppository (n = 39) groups. The follow-up occurred in three time periods (V1: -2~0 days; V2: 15-17 days; V3: 40 ± 3 days). At each visit, two vaginal swabs, one for clinical evaluation and one for laboratory examination, were taken from each patient. The Nugent score, Donders’ score, drug-related complications, recurrence rates, and microecological changes of vaginal swabs were assessed in the time three periods. Results At baseline, the two groups were similar in frequency of presentation with vaginal burning, odor, abnormal discharge, and itching. No meaningful differences in Nugent and Donders’ scores were detected between the two groups at stage V2 (Nugent: p = 0.67; Donders’: p = 0.85) and V3 (Nugent: p = 0.97; Donders: p = 0.55). The Furong group presented fewer complications compared to the Clindamycin group. However, this difference was not statistically significant (p = 0.15). Additionally, Accu16S indicated that the total abundance of bacteria in both groups sharply decreased in stage V2, but slightly increased in V3. In stage V3, the absolute abundance of Lactobacillus in the Furong group was considerably higher compared to untreated samples (p < 0.05). On the other hand, no momentous increase was detected in the Clindamycin group (p > 0.05). Conclusion Fufang Furong Effervescent Suppository can be as effective as clindamycin cream in the management of AV+BV while may restore the vagina microecosystem better.
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Affiliation(s)
- Meng Li
- School of Clinical Medicine, Tsinghua University, Beijing, China
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhen Zeng
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Huijun Feng
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yang Cao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Qiongqiong Zhang
- School of Clinical Medicine, Tsinghua University, Beijing, China
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Tao Lv
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Xingsheng Yang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, China
| | - Dianrong Song
- Gynecological Department, The First Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ping Li
- Department of Obstetrics and Gynecology, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lina Hu
- Department of Gynecology, The Second Hospital Affiliated to Chongqing Medical University, Chongqing, China
| | - Shangrong Fan
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ruifang An
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Bei Zhang
- Department of Obstetrics and Gynaecology, Xuzhou Central Hospital, Affiliated Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, China
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- *Correspondence: Qinping Liao, ; Lei Zhang,
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- *Correspondence: Qinping Liao, ; Lei Zhang,
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