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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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Moulia V, Ait-Mouheb N, Lesage G, Hamelin J, Wéry N, Bru-Adan V, Kechichian L, Heran M. Short-term effect of reclaimed wastewater quality gradient on soil microbiome during irrigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166028. [PMID: 37549700 DOI: 10.1016/j.scitotenv.2023.166028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
To investigate the effect of wastewater (WW) treatment on soil bacterial communities, water of different quality was used to irrigate eight lettuces per tank: raw municipal wastewater (RWW), WW treated with an aerated constructed wetland (CWW) and WW treated with a membrane bioreactor (MBW), and tap water (TW). The physicochemical and microbiological characteristics (quality indicators) of these water types were characterized, and the water and soil bacterial communities were monitored by quantitative PCR (qPCR) and 16S rRNA gene sequencing. Despite marked differences in microbial load and diversity of waters, soil communities remained remarkably stable after irrigation. Microbial biomass was increased only in soils irrigated with RWW. At the end of the irrigation period (day 84), soil and water shared a large fraction of their bacterial communities, from 43 % to 70 %, depending on the water quality, indicating a transfer of bacterial communities from water to soil. Overall, the relative abundance of Proteobacteria and Acidobacteria was increased and that of Actinobacteria was decreased in soils irrigated with MBW, CWW and even more with RWW. Multivariate ordination clearly separated soils in three groups: soils irrigated with the cleanest water (TW), with treated WW (MBW and CWW), and with untreated WW (RWW). Nitrifying, denitrifying, and nitrogen-fixing bacteria were quantified by qPCR targeting amoA, narG, and nifH, respectively. Nitrifying bacteria were the most affected by the water quality, as indicated by amoA copy number increase in RWW-irrigated soil and decrease in CWW-irrigated soil. Overall, the abundance of all three genes was positively influenced by RWW treatment. In conclusion, the 84 days of irrigation influenced the soil microbial communities, and the impact depended on the quality of the used water.
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Affiliation(s)
- V Moulia
- IEM, University of Montpellier, Montpellier, France; INRAE, UMR G-EAU, University of Montpellier, Montpellier, France; INRAE, Univ Montpellier, LBE, 102 avenue des Étangs, 11100, Narbonne, France
| | - N Ait-Mouheb
- INRAE, UMR G-EAU, University of Montpellier, Montpellier, France
| | - G Lesage
- IEM, University of Montpellier, Montpellier, France
| | - J Hamelin
- INRAE, Univ Montpellier, LBE, 102 avenue des Étangs, 11100, Narbonne, France
| | - N Wéry
- INRAE, Univ Montpellier, LBE, 102 avenue des Étangs, 11100, Narbonne, France.
| | - V Bru-Adan
- INRAE, Univ Montpellier, LBE, 102 avenue des Étangs, 11100, Narbonne, France
| | - L Kechichian
- INRAE, UMR G-EAU, University of Montpellier, Montpellier, France
| | - M Heran
- IEM, University of Montpellier, Montpellier, France
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Huang L, Levintal E, Erikson CB, Coyotl A, Horwath WR, Dahlke HE, Mazza Rodrigues JL. Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11084-11095. [PMID: 37467434 PMCID: PMC10399200 DOI: 10.1021/acs.est.3c01356] [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: 03/01/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023]
Abstract
Nitrate (NO3-) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3- leaching outcomes. We combine natural dual isotopes of NO3- (15N/14N and 18O/16O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3- leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of 15N-NO3- and 18O-NO3- after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3- being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3- leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3- changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3- leaching in agroecosystems.
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Affiliation(s)
- Laibin Huang
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - Elad Levintal
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - Christian Bernard Erikson
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - Adolfo Coyotl
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - William R. Horwath
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - Helen E. Dahlke
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
| | - Jorge L. Mazza Rodrigues
- Department
of Land, Air, and Water Resources, University
of California, Davis, Davis, California 95616, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
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Ding H, Liu T, Hu Q, Liu M, Cai M, Jiang Y, Cao C. Effect of microbial community structures and metabolite profile on greenhouse gas emissions in rice varieties. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119365. [PMID: 35489537 DOI: 10.1016/j.envpol.2022.119365] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 04/01/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Rice paddy fields are major sources of atmospheric methane (CH4) and nitrous oxide (N2O). Rice variety is an important factor affecting CH4 and N2O emissions. However, the interactive effects of rice metabolites and microorganisms on CH4 and N2O emissions in paddy fields are not clearly understood. In this study, a high greenhouse gas-emitting cultivar (YL 6) and a low greenhouse gas-emitting cultivar (YY 1540) were used as experimental materials. Metabolomics was used to examine the roots, root exudates, and bulk soil metabolites. High-throughput sequencing was used to determine the microbial community composition. YY 1540 had more secondary metabolites (flavonoids and isoflavonoids) in root exudates than YL 6. It was enriched with the uncultured members of the families Gemmatimonadanceae and Rhizobiales_Incertae_Sedis in bulk soil, and genera Burkholderia-Caballeronia-Paraburkholderia, Magnetospirillum, Aeromonas, and Anaeromyxobacter in roots, contributing to increased expression of pmoA and nosZ genes and reducing CH4 and N2O emissions. YL 6 roots and root exudates contained higher contents of carbohydrates [e.g., 6-O- acetylarbutin and 2-(3- hydroxyphenyl) ethanol 1'-glucoside] than those of YY 1540. They were enriched with genera RBG-16-58-14 in bulk soil and Exiguobacterium, and uncultured member of the Kineosporiaceae family in roots, which contributed to increased expression of mcrA, ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nirS, and nirK genes and greenhouse gas emissions. In general, these results established a link between metabolites, microorganisms, microbial functional genes, and greenhouse gas emissions. The metabolites of root exudates and roots regulated CH4 and N2O emissions by influencing the microbial community composition in bulk soil and roots.
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Affiliation(s)
- Huina Ding
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tianqi Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Quanyi Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Min Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mingli Cai
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yang Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Cougui Cao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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Wongkiew S, Chaikaew P, Takrattanasaran N, Khamkajorn T. Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management. Sci Rep 2022; 12:7368. [PMID: 35513414 PMCID: PMC9072534 DOI: 10.1038/s41598-022-09818-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.
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Affiliation(s)
- Sumeth Wongkiew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Water Science and Technology for Sustainable Environment Research Group, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Pasicha Chaikaew
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
| | - Natta Takrattanasaran
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
| | - Thanachanok Khamkajorn
- Land Development Department, Land Development Regional Office 1, Pathum Thani, 12110, Thailand
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Li H, Wang N, Ding J, Liu Y, Ding X, Wei Y, Li J, Ding GC. Spatial Distribution of the Pepper Blight ( Phytophthora capsici) Suppressive Microbiome in the Rhizosphere. FRONTIERS IN PLANT SCIENCE 2022; 12:748542. [PMID: 35126404 PMCID: PMC8813743 DOI: 10.3389/fpls.2021.748542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
The properties of plant rhizosphere are dynamic and heterogeneous, serving as different habitat filters for or against certain microorganisms. Herein, we studied the spatial distribution of bacterial communities in the rhizosphere of pepper plants treated with a disease-suppressive or non-suppressive soil. The bacterial richness was significantly (p < 0.05) higher in plants treated with the disease-suppressive soil than in those treated with the non-suppressive soil. Bacterial richness and evenness greatly differed between root parts, with decrease from the upper taproot to the upper fibrous root, the lower taproot, and the lower fibrous root. As expected, the bacterial community in the rhizosphere differed between suppressive and non-suppressive soil. However, the spatial variation (36%) of the bacterial community in the rhizosphere was much greater than that explained by soils (10%). Taxa such as subgroups of Acidobacteria, Nitrosospira, and Nitrospira were known to be selectively enriched in the upper taproot. In vitro Bacillus antagonists against Phytophthora capsici were also preferentially colonized in the taproot, while the genera such as Clostridium, Rhizobium, Azotobacter, Hydrogenophaga, and Magnetospirillum were enriched in the lower taproot or fibrous root. In conclusion, the spatial distribution of bacterial taxa and antagonists in the rhizosphere of pepper sheds light on our understanding of microbial ecology in the rhizosphere.
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Affiliation(s)
- Huixiu Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Tangshan Normal University, Tangshan, China
| | - Ning Wang
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Jia Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Yingjie Liu
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
| | - Xiaoyan Ding
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Yuquan Wei
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Ji Li
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
| | - Guo-chun Ding
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Science, China Agricultural University, Beijing, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Suzhou, China
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