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Chen C, Gong H, Wei Y, Xu T, Li J, Ding GC. Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy. BIORESOURCE TECHNOLOGY 2024; 401:130746. [PMID: 38679240 DOI: 10.1016/j.biortech.2024.130746] [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: 01/30/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.
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Affiliation(s)
- Chen Chen
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; National Observation and Research Station for Yangtze Estuarine Wetland Ecosystems, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haiqing Gong
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China
| | - Yuquan Wei
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ting Xu
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Ji Li
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, State Key Laboratory of Nutrient Use and Management, China Agricultural University, Beijing 100193, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Jiangsu Province 215128, China.
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Gong J, Liu B, Liu P, Zhang L, Chen C, Wei Y, Li J, Ding GC. Changes in bacterial diversity, co-occurrence pattern, and potential pathogens following digestate fertilization: Extending pathogen management to field for anaerobic digestion of livestock manure. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 158:107-115. [PMID: 36652821 DOI: 10.1016/j.wasman.2023.01.010] [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: 10/12/2022] [Revised: 12/01/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Digestate can spread pathogens into agroecosystem, posing serious threats to public health. However, the effect of digestate fertilization on digestate- or soil-borne pathogens has not been fully explored. Herein, two settings of microcosm experiment were performed with arable soil and digestate collected at two sites (Beilangzhong or Shunyi) to dissect the succession of the total and potential pathogenic bacterial communities following digestate fertilization. Each experimental setting consisted of three treatments, including digestate aerobically incubated in sterilized soil, and soil amended with sterilized or non-sterilized digestate. Digestate-borne potential pathogenic bacteria were enriched after the aerobic incubation, with Streptococcus sobrinus in the Beilangzhong setting, and Escherichia coli and Enterococcus faecium in the Shunyi setting. Potential soil-borne pathogenic bacteria, such as Acinetobacter lowffii and Pseudomonas fluorescens, were stimulated by the sterilized digestate in the Shunyi setting. Interestingly, S. sobrinus, E. coli, and Ent. faecium did not increase when digestate was amended into the non-sterilized soil, suggesting that soil microorganisms can inhibit the resurgence of these digestate-borne pathogens. A large-scale survey further revealed that organic fertilization exerted a site-dependent effect on different species of potential pathogen, but it did not enrich the total relative abundance of potential pathogenic bacteria in soils. Collectively, these results highlight that pathogen management of anaerobic digestion of livestock manure needs to be extended from anaerobic reactor to field.
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Affiliation(s)
- Jingyang Gong
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Xinyang Agriculture and Forestry University, Xinyang, China
| | - Baojun Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Pingping Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Lina Zhang
- Jiangsu Coastal Area Institute of Agricultural Science, Yancheng, China
| | - Chen Chen
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128 Jiangsu Province, China.
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Martínez-Yáñez MG, Silva-Ortega CO, Hernández-Aranda VA, Vallejo-Pérez MR, Alcalá-Briseño R, Vega-Manriquez DX, Aguilar-Benítez G, Jarquin-Gálvez R, Lara-Ávila JP. Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02156-9. [PMID: 36520176 DOI: 10.1007/s00248-022-02156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.
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Affiliation(s)
| | | | | | - Moisés Roberto Vallejo-Pérez
- CONACYT, Universidad Autónoma de San Luis Potosí. Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), San Luis Potosí, SLP, México
| | | | - Delia Xochil Vega-Manriquez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - Gisela Aguilar-Benítez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - Ramón Jarquin-Gálvez
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México
| | - José Pablo Lara-Ávila
- Facultad de Agronomía y Veterinaria, Universidad Autónoma de San Luis Potosí, Soledad de Graciano Sánchez, SLP, México.
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Guajardo-Leiva S, Alarcón J, Gutzwiller F, Gallardo-Cerda J, Acuña-Rodríguez IS, Molina-Montenegro M, Crandall KA, Pérez-Losada M, Castro-Nallar E. Source and acquisition of rhizosphere microbes in Antarctic vascular plants. Front Microbiol 2022; 13:916210. [PMID: 36160194 PMCID: PMC9493328 DOI: 10.3389/fmicb.2022.916210] [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: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Jaime Alarcón
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Florence Gutzwiller
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Jorge Gallardo-Cerda
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | | | - Marco Molina-Montenegro
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigación en Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC, United States
- Division of Emergency Medicine, Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Children’s National Hospital, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
- *Correspondence: Eduardo Castro-Nallar,
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Zhang Z, Xiao YS, Zhan Y, Zhang Z, Liu Y, Wei Y, Xu T, Li J. Tomato microbiome under long-term organic and conventional farming. IMETA 2022; 1:e48. [PMID: 38868718 PMCID: PMC10989780 DOI: 10.1002/imt2.48] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 06/14/2024]
Abstract
The compartment niche is the main reason behind the shifts in endophytic bacterial communities. Long-term organic greenhouse exerted limited influence on the variations of endophytic bacterial communities. Organic greenhouse and root had more complex co-occurrence networks than conventional greenhouse and stem, respectively. Cultivable method results found that Protecbacteria, Bacteriodes, and Actinobacteria are the dominant phyla in the endophytes.
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Affiliation(s)
- Zeyu Zhang
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Yang Sean Xiao
- College of Water Resources and Civil EngineeringChina Agricultural UniversityBeijingChina
| | - Yabin Zhan
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Zengqiang Zhang
- College of Resources and Environmental ScienceNorthwest A&F UniversityYanglinChina
| | - Youzhou Liu
- Institute of Plant ProtectionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yuquan Wei
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Ting Xu
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
| | - Ji Li
- College of Resources and Environmental ScienceChina Agricultural UniversityBeijingChina
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Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions. Int J Mol Sci 2022; 23:ijms23158820. [PMID: 35955951 PMCID: PMC9369415 DOI: 10.3390/ijms23158820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 12/13/2022] Open
Abstract
The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.
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