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Ornik M, Salinas R, Antonacci G, Schädler M, Azarbad H. The stress history of soil bacteria under organic farming enhances the growth of wheat seedlings. Front Microbiol 2024; 15:1355158. [PMID: 38577685 PMCID: PMC10993729 DOI: 10.3389/fmicb.2024.1355158] [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: 12/13/2023] [Accepted: 03/04/2024] [Indexed: 04/06/2024] Open
Abstract
The effects of stress factors associated with climate change and agricultural management practices on microorganisms are often studied separately, and it remains to be determined how these factors impact the soil microbiome and, subsequently, plant growth characteristics. The aim of this study was to understand how the historical climate and agriculture to which soil microbes have been exposed can influence the growth characteristics of wheat seedlings and their associated bacterial communities. We collected soil from organic and conventional fields with different histories of climate conditions to extract microbes to inoculate wheat seeds under agar-based cultivation conditions. Within a growth period of 8 days, we monitored germination rates and time as well as seedling above-ground biomass and their associated bacterial communities. The results showed a positive interaction between conventional farming practices and an ambient climate for faster and higher germination rates. We demonstrate that soil microbial extracts from organic farming with experience of the future climate significantly enhanced above-ground biomass along with the diversity of bacterial communities associated with seedlings than other treatments. Such findings support the idea that organic agricultural practices not only mitigate the adverse effects of climate change but also promote the diversity of seedling-associated bacteria.
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Affiliation(s)
- Muriel Ornik
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
| | - Renata Salinas
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
| | - Giona Antonacci
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
| | - Martin Schädler
- Department of Community Ecology, Helmholtz-Centre for Environmental Research – UFZ, Halle, Germany
- iDiv – Centre for Integrative Biodiversity Research Halle-Leipzig-Jena, Leipzig, Germany
| | - Hamed Azarbad
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
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Wang Y, Zhao X, Omidvar N, Liu M, Zou D, Zhang M. Insight into functional mechanisms of percarbamide and nitrification inhibitors in degrading fungicide residues and shaping microbial communities in soil-plant systems. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118687. [PMID: 37517094 DOI: 10.1016/j.jenvman.2023.118687] [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: 05/03/2023] [Revised: 07/03/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
Fungicides and nitrogen (N) fertilizers are essential to maintain plant yield in current intensive agriculture. Percarbamide is a novel type of N fertilizer with strong oxidizing property, and the nitrification inhibitor is widely used in agricultural production. It may be feasible to apply percarbamide and nitrification inhibitor as N management to promote fungicide dissipations in soil-plant system. This study quantified the effects of percarbamide and nitrification inhibitor dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP) on carbendazim residues, and microbial communities of soil-plant systems, and relationships among carbendazim residues, soil and endophytic microbial communities and plant yields were also comprehensively quantified. Compared with the control, the percarbamide significantly reduced soil carbendazim residues by 29.4% but enhanced the lettuce yield by 28.0%. Soil carbendazim residues were significantly and negatively correlated with the soil total N and NO3--N contents. Soil microbial community structures and co-occurrence networks were more sensitive to N management than their endophytic counterparts. In comparison to the percarbamide alone, the DCD significantly increased the nodes of soil fungal community co-occurrence network which were positively correlated with the plant yield. The DCD outweighed DMPP in increasing the lettuce yield and soil fungal community stability and reshaping soil bacterial community structure. Our study suggested that soil microbial communities were more sensitive to percarbamide and nitrification inhibitor applications than their endophytic counterparts under fungicide pressure and that the DCD outweighed DMPP in reshaping microbial communities. The integrated applications of percarbamide and nitrification inhibitors were promising soil N management strategies to promote fungicide removal and stimulate microbial community in the soil-plant systems.
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Affiliation(s)
- Yan Wang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, China
| | - Xinlin Zhao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Negar Omidvar
- Centre for Planetary Health and Food Security, Griffith University, Nathan, Brisbane, QLD, 4111, Australia
| | - Mengting Liu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, China
| | - Dongsheng Zou
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, China
| | - Manyun Zhang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, 410128, China; Centre for Planetary Health and Food Security, Griffith University, Nathan, Brisbane, QLD, 4111, Australia.
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Bei Q, Reitz T, Schnabel B, Eisenhauer N, Schädler M, Buscot F, Heintz-Buschart A. Extreme summers impact cropland and grassland soil microbiomes. THE ISME JOURNAL 2023; 17:1589-1600. [PMID: 37419993 PMCID: PMC10504347 DOI: 10.1038/s41396-023-01470-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.
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Affiliation(s)
- Qicheng Bei
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany.
| | - Thomas Reitz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Beatrix Schnabel
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Azarbad H. Conventional vs. Organic Agriculture-Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates? Front Microbiol 2022; 13:903500. [PMID: 35814715 PMCID: PMC9261957 DOI: 10.3389/fmicb.2022.903500] [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: 03/24/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years, agricultural productivity has been affected dramatically by climate-related events such as drought. On the other hand, agricultural intensification is expected to increase to satisfy the need for increased global food production. Microbes associated with soil and plants produce a range of bioactive natural products that significantly contribute to crop stress tolerance. Therefore, a better understanding of the parallel effects of agricultural management (conventional and organic croplands) and climate conditions on soil-microbe-plant interactions is crucial to maximizing the effort in engineering a plant microbiome that can better support productivity in agroecosystems. This paper provides a general overview of the major current debates on conventional and organic farming performance regarding yields, particularly under ambient and future climate conditions. With the main focus on cropland, the effect of agricultural management on soil and plant microbiomes is discussed. In addition, the advantage of incorporating microbiome-based approaches into current farming practices to ensure agricultural productivity with less adverse environmental impacts is highlighted. To enhance crop production under organic farming without massive land-use changes and expansion of farmland, the microbial-based approach can be used to ensure higher productivity, particularly under a rapidly changing climate.
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Affiliation(s)
- Hamed Azarbad
- Department of Biology, Evolutionary Ecology of Plants, Philipps-University Marburg, Marburg, Germany
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Zhang Y, Xie Y, Ma H, Zhang J, Jing L, Wang Y, Li J. The Influence of Climate Warming and Humidity on Plant Diversity and Soil Bacteria and Fungi Diversity in Desert Grassland. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122580. [PMID: 34961051 PMCID: PMC8707519 DOI: 10.3390/plants10122580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Our study, which was conducted in the desert grassland of Ningxia in China (E 107.285, N 37.763), involved an experiment with five levels of annual precipitation 33% (R33), 66% (R66), 100% (CK), 133% (R133), 166% (R166) and two temperature levels (inside Open-Top Chamber (OTC) and outside OTC). Our objective was to determine how plant, soil bacteria, and fungi diversity respond to climate change. Our study suggested that plant α-diversity in CK and TCK were significantly higher than that of other treatments. Increased precipitation promoted root biomass (RB) growth more than aboveground living biomass (ALB). R166 promoted the biomass of Agropyron mongolicum the most. In the fungi communities, temperature and precipitation interaction promoted α-diversity. In the fungi communities, the combination of increased temperature and natural precipitation (TCK) promoted β-diversity the most, whose distance was determined to be 25,124 according to PCA. In the bacteria communities, β-diversity in CK was significantly higher than in other treatments, and the distance was determined to be 3010 according to PCA. Soil bacteria and fungi α- and β-diversity, and ALB promoted plant diversity the most. The interactive effects of temperature and precipitation on C, N, and P contents of plants were larger than their independent effects.
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Affiliation(s)
- Yi Zhang
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
| | - Yingzhong Xie
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
- State Key Laboratory Cultivation Base for Northwest Degraded Ecosystem Recovery and Reconstruction, Yinchuan 750021, China
| | - Hongbin Ma
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
- State Key Laboratory Cultivation Base for Northwest Degraded Ecosystem Recovery and Reconstruction, Yinchuan 750021, China
| | - Juan Zhang
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
| | - Le Jing
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
| | - Yutao Wang
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
| | - Jianping Li
- College of Agriculture, Ningxia University, Yinchuan 750021, China; (Y.Z.); (Y.X.); (H.M.); (J.Z.); (L.J.); (Y.W.)
- State Key Laboratory Cultivation Base for Northwest Degraded Ecosystem Recovery and Reconstruction, Yinchuan 750021, China
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