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Martin FM, van der Heijden MGA. The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application. New Phytol 2024; 242:1486-1506. [PMID: 38297461 DOI: 10.1111/nph.19541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.
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Affiliation(s)
- Francis M Martin
- Université de Lorraine, INRAE, UMR IAM, Champenoux, 54280, France
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Marcel G A van der Heijden
- Department of Agroecology & Environment, Plant-Soil Interactions, Agroscope, Zürich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8057, Switzerland
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2
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Peng Z, Qian X, Liu Y, Li X, Gao H, An Y, Qi J, Jiang L, Zhang Y, Chen S, Pan H, Chen B, Liang C, van der Heijden MGA, Wei G, Jiao S. Land conversion to agriculture induces taxonomic homogenization of soil microbial communities globally. Nat Commun 2024; 15:3624. [PMID: 38684659 PMCID: PMC11058813 DOI: 10.1038/s41467-024-47348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Agriculture contributes to a decline in local species diversity and to above- and below-ground biotic homogenization. Here, we conduct a continental survey using 1185 soil samples and compare microbial communities from natural ecosystems (forest, grassland, and wetland) with converted agricultural land. We combine our continental survey results with a global meta-analysis of available sequencing data that cover more than 2400 samples across six continents. Our combined results demonstrate that land conversion to agricultural land results in taxonomic and functional homogenization of soil bacteria, mainly driven by the increase in the geographic ranges of taxa in croplands. We find that 20% of phylotypes are decreased and 23% are increased by land conversion, with croplands enriched in Chloroflexi, Gemmatimonadota, Planctomycetota, Myxcoccota and Latescibacterota. Although there is no significant difference in functional composition between natural ecosystems and agricultural land, functional genes involved in nitrogen fixation, phosphorus mineralization and transportation are depleted in cropland. Our results provide a global insight into the consequences of land-use change on soil microbial taxonomic and functional diversity.
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Affiliation(s)
- Ziheng Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yu Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Xiaomeng Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Hang Gao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yining An
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Jiejun Qi
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Lan Jiang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Yiran Zhang
- College of Natural Resources and Environment, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Shi Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Haibo Pan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Beibei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Chunling Liang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gehong Wei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
| | - Shuo Jiao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, 712100, Yangling, Shaanxi, P. R. China.
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Richter F, Calonne-Salmon M, van der Heijden MGA, Declerck S, Stanley CE. AMF-SporeChip provides new insights into arbuscular mycorrhizal fungal asymbiotic hyphal growth dynamics at the cellular level. Lab Chip 2024; 24:1930-1946. [PMID: 38416560 DOI: 10.1039/d3lc00859b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and anastomosis/hyphal healing mechanisms. To fill existing gaps in AMF knowledge, we developed a new microfluidic platform - the AMF-SporeChip - to visualise the foraging behaviour of germinating Rhizophagus and Gigaspora spores and confront asymbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time. The AMF-SporeChip allowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF asymbiotic hyphae. We witnessed tip-to-tip and tip-to-side hyphal anastomosis formation. Anastomosis involved directed hyphal growth in a "stop-and-go" manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction, including the formation of up to 8 septa upon retraction, as part of a highly dynamic space navigation, probably evolved to optimise foraging efficiency. Our findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, the AMF-SporeChip is expected to open many future frontiers for AMF research.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Marcel G A van der Heijden
- Agroecology and Environment Research Division, Agroscope, 8046 Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- Institute of Environmental Biology, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Stéphane Declerck
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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Zhang C, van der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, Cosme M, Berendsen RL. Correction: A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. Microbiome 2024; 12:30. [PMID: 38374276 PMCID: PMC10875889 DOI: 10.1186/s40168-024-01776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Affiliation(s)
- Changfeng Zhang
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH‑8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH‑8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH‑8008, Zurich, Switzerland
| | - Bethany K Dodds
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Thi Bich Nguyen
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alain Valzano-Held
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH‑8046, Zürich, Switzerland
| | - Marco Cosme
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain‑La‑Neuve, Belgium
- Plants and Ecosystems, Biology Department, University of Antwerp, Antwerp, Belgium
| | - Roeland L Berendsen
- Plant‑Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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5
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Zhang C, de Pasquale S, Hartman K, Stanley CE, Berendsen RL, van der Heijden MGA. The microbial contribution to litter decomposition and plant growth. Environ Microbiol Rep 2024; 16:e13205. [PMID: 38018445 PMCID: PMC10866077 DOI: 10.1111/1758-2229.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/06/2023] [Indexed: 11/30/2023]
Abstract
Soil and plant roots are colonized by highly complex and diverse communities of microbes. It has been proposed that bacteria and fungi have synergistic effects on litter decomposition, but experimental evidence supporting this claim is weak. In this study, we manipulated the composition of two microbial kingdoms (Bacteria and Fungi) in experimental microcosms. In microcosms that were inoculated with fungi, litter loss was 47% higher than in microcosms that were not inoculated or only inoculated with bacteria. Combined inoculation with both bacteria and fungi did not significantly enhance decomposition compared with the fungi-only treatments, and, as such, we found no evidence for complementary effects using our experimental setup. Inoculation with fungi also had a positive impact on plant growth after 4 and 8 weeks (480% and 710% growth stimulation, respectively). After 16 weeks, plant biomass was highest in microcosms where both bacteria and fungi were present pointing to fungal-bacterial complementarity in stimulating plant growth. Overall, this study suggests that fungi are the main decomposers of plant litter and that the inoculated fungi contribute to plant growth in our experimental system.
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Affiliation(s)
- Changfeng Zhang
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Simone de Pasquale
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Kyle Hartman
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Claire E. Stanley
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
| | - Roeland L. Berendsen
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
| | - Marcel G. A. van der Heijden
- Plant‐Microbe Interactions, Department of Biology, Faculty of ScienceUtrecht UniversityUtrechtthe Netherlands
- Plant Soil InteractionsDivision Agroecology and Environment, AgroscopeZürichSwitzerland
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
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6
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Tedersoo L, van der Heijden MGA, Orgiazzi A. Interaction effects of pH and land cover on soil microbial diversity are climate-dependent. Environ Microbiol 2024; 26:e16572. [PMID: 38195068 DOI: 10.1111/1462-2920.16572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Factors regulating the diversity and composition of soil microbial communities include soil properties, land cover and climate. How these factors interact at large scale remains poorly investigated. Here, we used an extensive dataset including 715 locations from 24 European countries to investigate the interactive effects of climatic region, land cover and pH on soil bacteria and fungi. We found that differences in microbial diversity and community composition between land cover types depended on the climatic region. In Atlantic, Boreal and Continental regions, microbial richness was higher in croplands and grasslands than woodlands while richness in Mediterranean areas did not vary significantly among land cover types. These differences were further related to soil pH, as a driver of bacterial and fungal richness in most climatic regions, but the interaction of pH with land cover depended on the region. Microbial community composition differed the most between croplands and woodlands in all regions, mainly due to differences in pH. In the Mediterranean region, bacterial communities in woodlands and grasslands were the most similar, whereas in other regions, grassland and cropland-associated bacteria showed more similarity. Overall, we showed that key factors interact in shaping soil microbial communities in a climate-dependent way at large scale.
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Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- European Dynamics, Brussels, Belgium
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7
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Zhang C, van der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, Cosme M, Berendsen RL. A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. Microbiome 2024; 12:13. [PMID: 38243337 PMCID: PMC10799531 DOI: 10.1186/s40168-023-01726-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/18/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis. RESULTS Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization. CONCLUSIONS Our results highlight that AM fungi do not function in isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.
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Affiliation(s)
- Changfeng Zhang
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Bethany K Dodds
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Thi Bich Nguyen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alain Valzano-Held
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marco Cosme
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
- Plants and Ecosystems, Biology Department, University of Antwerp, Antwerp, Belgium
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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Lutz S, Bodenhausen N, Hess J, Valzano-Held A, Waelchli J, Deslandes-Hérold G, Schlaeppi K, van der Heijden MGA. Author Correction: Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat Microbiol 2023:10.1038/s41564-023-01577-7. [PMID: 38114743 DOI: 10.1038/s41564-023-01577-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Affiliation(s)
- Stefanie Lutz
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Julia Hess
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Alain Valzano-Held
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Jan Waelchli
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Gabriel Deslandes-Hérold
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland.
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Bender SF, Schulz S, Martínez-Cuesta R, Laughlin RJ, Kublik S, Pfeiffer-Zakharova K, Vestergaard G, Hartman K, Parladé E, Römbke J, Watson CJ, Schloter M, van der Heijden MGA. Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses. New Phytol 2023; 240:2020-2034. [PMID: 37700504 DOI: 10.1111/nph.19252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.
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Affiliation(s)
- S Franz Bender
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Rubén Martínez-Cuesta
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ronald J Laughlin
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Kristina Pfeiffer-Zakharova
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kyle Hartman
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jörg Römbke
- ECT Ökotoxikologie GmbH, Böttgerstr. 2-14, D-65439, Flörsheim, Germany
| | - Catherine J Watson
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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11
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Feng M, Varliero G, Qi W, Stierli B, Edwards A, Robinson S, van der Heijden MGA, Frey B. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environ Microbiol 2023; 25:3116-3138. [PMID: 37688461 DOI: 10.1111/1462-2920.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.
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Affiliation(s)
- Maomao Feng
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Serina Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil Interactions, Agroscope, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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12
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Lutz S, Bodenhausen N, Hess J, Valzano-Held A, Waelchli J, Deslandes-Hérold G, Schlaeppi K, van der Heijden MGA. Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi. Nat Microbiol 2023; 8:2277-2289. [PMID: 38030903 PMCID: PMC10730404 DOI: 10.1038/s41564-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Alternative solutions to mineral fertilizers and pesticides that reduce the environmental impact of agriculture are urgently needed. Arbuscular mycorrhizal fungi (AMF) can enhance plant nutrient uptake and reduce plant stress; yet, large-scale field inoculation trials with AMF are missing, and so far, results remain unpredictable. We conducted on-farm experiments in 54 fields in Switzerland and quantified the effects on maize growth. Growth response to AMF inoculation was highly variable, ranging from -12% to +40%. With few soil parameters and mainly soil microbiome indicators, we could successfully predict 86% of the variation in plant growth response to inoculation. The abundance of pathogenic fungi, rather than nutrient availability, best predicted (33%) AMF inoculation success. Our results indicate that soil microbiome indicators offer a sustainable biotechnological perspective to predict inoculation success at the beginning of the growing season. This predictability increases the profitability of microbiome engineering as a tool for sustainable agricultural management.
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Affiliation(s)
- Stefanie Lutz
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Natacha Bodenhausen
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Julia Hess
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Alain Valzano-Held
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Jan Waelchli
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Gabriel Deslandes-Hérold
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Biochemistry, Institute of Molecular Plant Biology, ETH Zurich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland.
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13
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Abstract
Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.
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Affiliation(s)
- Mark A. Anthony
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Forest Dynamics Research Unit, Birmensdorf8903, Switzerland
| | - S. Franz Bender
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich8008, Switzerland
| | - Marcel G. A. van der Heijden
- Plant-Soil Interactions Unit, Research Division Agroecology and Environment, Agroscope, Zürich8046, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich8008, Switzerland
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14
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Hartman K, Schmid MW, Bodenhausen N, Bender SF, Valzano-Held AY, Schlaeppi K, van der Heijden MGA. A symbiotic footprint in the plant root microbiome. Environ Microbiome 2023; 18:65. [PMID: 37525294 PMCID: PMC10391997 DOI: 10.1186/s40793-023-00521-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure. RESULTS We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts. CONCLUSION Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.
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Affiliation(s)
- Kyle Hartman
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | | | - Natacha Bodenhausen
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, 5070, Switzerland
| | - S Franz Bender
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Alain Y Valzano-Held
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland
| | - Klaus Schlaeppi
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland.
- Institute of Plant Sciences, Faculty of Science, University of Bern, Bern, 3013, Switzerland.
| | - Marcel G A van der Heijden
- Department of Agroecology and Environment, Plant Soil Interactions, Reckenholzstrasse 191, Agroscope, Zürich, 8046, Switzerland.
- Department of Plant and Microbial Biology, University of Zürich, Zürich, 8008, Switzerland.
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15
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Schmid MW, Mikryukov V, Dulya O, Tedersoo L, Bahram M, Lugato E, van der Heijden MGA, Orgiazzi A. Publisher Correction: Patterns in soil microbial diversity across Europe. Nat Commun 2023; 14:4298. [PMID: 37463906 PMCID: PMC10353981 DOI: 10.1038/s41467-023-39596-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Olesya Dulya
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emanuele Lugato
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
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16
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Riedo J, Yokota A, Walther B, Bartolomé N, van der Heijden MGA, Bucheli TD, Walder F. Temporal dynamics of total and bioavailable fungicide concentrations in soil and their effect upon nine soil microbial markers. Sci Total Environ 2023; 878:162995. [PMID: 36948305 DOI: 10.1016/j.scitotenv.2023.162995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 05/13/2023]
Abstract
Pesticides constitute an integral part of today's agriculture. Their widespread use leads to ubiquitous contamination of the environment, including soils. Soils are a precious resource providing vital functions to society - thus, it is of utmost importance to thoroughly assess the risk posed by widespread pesticide contamination. The exposure of non-target organisms to pesticides in soils is challenging to quantify since only a fraction of the total pesticide concentration is bioavailable. Here we measured and compared the bioavailable and total concentrations of three fungicides - boscalid, azoxystrobin, and epoxiconazole - and evaluated which concentration best predicts effects on nine microbial markers. The experiments were performed in three different soils at five time points over two months employing nearly 900 microcosms with a model plant. The total and bioavailable concentrations of azoxystrobin and boscalid decreased steadily during the trial to levels of 25 % and 8 % of the original concentration, respectively, while the concentration of epoxiconazole in soil nearly remained unchanged. The bioavailable fraction generally showed a slightly faster and more pronounced decline. The microbial markers varied in their sensitivity to the three fungicides. Specific microbial markers, such as arbuscular mycorrhizal fungi, and bacterial and archaeal ammonia oxidizers, were most sensitive to each of the fungicide treatments, making them suitable indicators for pesticide effects. Even though the responses were predominantly negative, they were also transient, and the impact was no longer evident after two months. Finally, the bioavailable fraction did not better predict the relationships between exposure and effect than the total concentration. This study demonstrates that key microbial groups are temporarily susceptible to a single fungicide application, pointing to the risk that repeated use of pesticides may disrupt vital soil functions such as nutrient cycling in agroecosystems.
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Affiliation(s)
- Judith Riedo
- Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Aya Yokota
- Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Barbara Walther
- Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Nora Bartolomé
- Division of Methods Development and Analytics, Agroscope, 8046 Zurich, Switzerland
| | - Marcel G A van der Heijden
- Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
| | - Thomas D Bucheli
- Division of Methods Development and Analytics, Agroscope, 8046 Zurich, Switzerland.
| | - Florian Walder
- Division of Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland.
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17
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Labouyrie M, Ballabio C, Romero F, Panagos P, Jones A, Schmid MW, Mikryukov V, Dulya O, Tedersoo L, Bahram M, Lugato E, van der Heijden MGA, Orgiazzi A. Patterns in soil microbial diversity across Europe. Nat Commun 2023; 14:3311. [PMID: 37291086 PMCID: PMC10250377 DOI: 10.1038/s41467-023-37937-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/10/2023] Open
Abstract
Factors driving microbial community composition and diversity are well established but the relationship with microbial functioning is poorly understood, especially at large scales. We analysed microbial biodiversity metrics and distribution of potential functional groups along a gradient of increasing land-use perturbation, detecting over 79,000 bacterial and 25,000 fungal OTUs in 715 sites across 24 European countries. We found the lowest bacterial and fungal diversity in less-disturbed environments (woodlands) compared to grasslands and highly-disturbed environments (croplands). Highly-disturbed environments contain significantly more bacterial chemoheterotrophs, harbour a higher proportion of fungal plant pathogens and saprotrophs, and have less beneficial fungal plant symbionts compared to woodlands and extensively-managed grasslands. Spatial patterns of microbial communities and predicted functions are best explained when interactions among the major determinants (vegetation cover, climate, soil properties) are considered. We propose guidelines for environmental policy actions and argue that taxonomical and functional diversity should be considered simultaneously for monitoring purposes.
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Affiliation(s)
- Maëva Labouyrie
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | | | - Ferran Romero
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland
| | - Panos Panagos
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | | | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Olesya Dulya
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Emanuele Lugato
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland.
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Zürich, Switzerland.
| | - Alberto Orgiazzi
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
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18
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Edlinger A, Garland G, Banerjee S, Degrune F, García-Palacios P, Herzog C, Pescador DS, Romdhane S, Ryo M, Saghaï A, Hallin S, Maestre FT, Philippot L, Rillig MC, van der Heijden MGA. The impact of agricultural management on soil aggregation and carbon storage is regulated by climatic thresholds across a 3000 km European gradient. Glob Chang Biol 2023; 29:3177-3192. [PMID: 36897740 DOI: 10.1111/gcb.16677] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/07/2023] [Indexed: 05/03/2023]
Abstract
Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (-56%) and SOC stocks (-35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.
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Affiliation(s)
- Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Environmental System Science, ETH Zurich, Zurich, Switzerland
| | - Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Soil Science and Environment Group, Changins, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - David Sánchez Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Sana Romdhane
- Department of Agroecology, INRA, AgroSup Dijon, University Bourgogne Franche Comte, Dijon, France
| | - Masahiro Ryo
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
- Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain
- Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - Laurent Philippot
- Department of Agroecology, INRA, AgroSup Dijon, University Bourgogne Franche Comte, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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19
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Romero F, Hilfiker S, Edlinger A, Held A, Hartman K, Labouyrie M, van der Heijden MGA. Soil microbial biodiversity promotes crop productivity and agro-ecosystem functioning in experimental microcosms. Sci Total Environ 2023; 885:163683. [PMID: 37142020 DOI: 10.1016/j.scitotenv.2023.163683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/06/2023]
Abstract
Soil biota contribute substantially to multiple ecosystem functions that are key for geochemical cycles and plant performance. However, soil biodiversity is currently threatened by land-use intensification, and a mechanistic understanding of how soil biodiversity loss interacts with the myriad of intensification elements (e.g., the application of chemical fertilizers) is still unresolved. Here we experimentally simplified soil biological communities in microcosms to test whether changes in the soil microbiome influenced soil multifunctionality including crop productivity (leek, Allium porrum). Additionally, half of microcosms were fertilized to further explore how different levels of soil biodiversity interact with nutrient additions. Our experimental manipulation achieved a significant reduction of soil alpha-diversity (45.9 % reduction in bacterial richness, 82.9 % reduction in eukaryote richness) and resulted in the complete removal of key taxa (i.e., arbuscular mycorrhizal fungi). Soil community simplification led to an overall decrease in ecosystem multifunctionality; particularly, plant productivity and soil nutrient retention capacity were reduced with reduced levels of soil biodiversity. Ecosystem multifunctionality was positively correlated with soil biodiversity (R = 0.79). Mineral fertilizer application had little effect on multifunctionality compared to soil biodiversity reduction, but it reduced leek nitrogen uptake from decomposing litter by 38.8 %. This suggests that natural processes and organic nitrogen acquisition are impaired by fertilization. Random forest analyses revealed a few members of protists (i.e., Paraflabellula), Actinobacteria (i.e., Micolunatus), and Firmicutes (i.e., Bacillus) as indicators of ecosystem multifunctionality. Our results suggest that preserving the diversity of soil bacterial and eukaryotic communities within agroecosystems is crucial to ensure the provisioning of multiple ecosystem functions, particularly those directly related to essential ecosystem services such as food provision.
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Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland.
| | - Sarah Hilfiker
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Anna Edlinger
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Alain Held
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Kyle Hartman
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland
| | - Maëva Labouyrie
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; European Commission, Joint Research Centre Ispra (JRC Ispra), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, 8046 Zurich, Switzerland; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.
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20
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Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, Bastida F, Moreno-Jiménez E, Zhou XQ, Hu HW, He JZ, Moreno JL, Abades S, Alfaro F, Bamigboye AR, Berdugo M, Blanco-Pastor JL, de Los Ríos A, Duran J, Grebenc T, Illán JG, Makhalanyane TP, Molina-Montenegro MA, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Teixido AL, Casado-Coy N, Trivedi P, Torres-Díaz C, Verma JP, Mukherjee A, Zeng XM, Wang L, Wang J, Zaady E, Zhou X, Huang Q, Tan W, Zhu YG, Rillig MC, Delgado-Baquerizo M. Publisher Correction: Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat Commun 2023; 14:2405. [PMID: 37100778 PMCID: PMC10133300 DOI: 10.1038/s41467-023-37920-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Agroscope, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Judith Riedo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Carlos Sanz-Lazaro
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
- Department of Ecology, University of Alicante, PO Box 99, Alicante, E-03080, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Eduardo Moreno-Jiménez
- Department of Agricultural and Food Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hang-Wei Hu
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Ji-Zheng He
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, 7800003, CP, Chile
| | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Miguel Berdugo
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense de Madrid, C/Jose Antonio Novais 12, Madrid, 28040, Spain
| | | | - Asunción de Los Ríos
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - Jorge Duran
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, 99164 USA, USA
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, DSI/NRF SARChI Chair in Marine Microbiomics, University of Pretoria, Pretoria, 0028, South Africa
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology, ICB, Universidad de Talca, Talca, Chile
- CEAZA, Universidad Católica del Norte, Coquimbo, Chile
| | - Tina U Nahberger
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Gabriel F Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, MG, Brazil
| | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Alexandra Rodríguez
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, 04510, CP, México
| | - Alberto L Teixido
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Av. Fernando Corrêa, 2367, Boa Esperança, Cuiabá, 78060-900, MT, Brazil
| | - Nuria Casado-Coy
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, 80523, CO, USA
| | - Cristian Torres-Díaz
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias. Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Jay Prakash Verma
- Plant-Microbes Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Arpan Mukherjee
- Plant-Microbes Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Xiao-Min Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Wang
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Jianyong Wang
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, 8531100, Israel
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan, 430000, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, E-41012, Spain.
- Unidad Asociada CSIC-UPO (BioFun)., Universidad Pablo de Olavide, Sevilla, 41013, Spain.
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21
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Liu YR, van der Heijden MGA, Riedo J, Sanz-Lazaro C, Eldridge DJ, Bastida F, Moreno-Jiménez E, Zhou XQ, Hu HW, He JZ, Moreno JL, Abades S, Alfaro F, Bamigboye AR, Berdugo M, Blanco-Pastor JL, de Los Ríos A, Duran J, Grebenc T, Illán JG, Makhalanyane TP, Molina-Montenegro MA, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Rey A, Rodríguez A, Siebe C, Teixido AL, Casado-Coy N, Trivedi P, Torres-Díaz C, Verma JP, Mukherjee A, Zeng XM, Wang L, Wang J, Zaady E, Zhou X, Huang Q, Tan W, Zhu YG, Rillig MC, Delgado-Baquerizo M. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide. Nat Commun 2023; 14:1706. [PMID: 36973286 PMCID: PMC10042830 DOI: 10.1038/s41467-023-37428-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.
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Affiliation(s)
- Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Agroscope, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Judith Riedo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Carlos Sanz-Lazaro
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
- Department of Ecology, University of Alicante, PO Box 99, Alicante, E-03080, Spain
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Eduardo Moreno-Jiménez
- Department of Agricultural and Food Chemistry, Faculty of Sciences, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hang-Wei Hu
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - Ji-Zheng He
- Faculty of Science, The University of Melbourne, Parkville, 3010, VIC, Australia
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100, Murcia, Spain
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
| | - Fernando Alfaro
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Santiago, Chile
- Instituto de Ecología y Biodiversidad (IEB), Santiago, 7800003, CP, Chile
| | - Adebola R Bamigboye
- Natural History Museum (Botany Unit), Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Miguel Berdugo
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense de Madrid, C/Jose Antonio Novais 12, Madrid, 28040, Spain
| | | | - Asunción de Los Ríos
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - Jorge Duran
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Tine Grebenc
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, Washington State University, Pullman, WA, 99164 USA, USA
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, DSI/NRF SARChI Chair in Marine Microbiomics, University of Pretoria, Pretoria, 0028, South Africa
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology, ICB, Universidad de Talca, Talca, Chile
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, 31270-901, MG, Brazil
| | - Tina U Nahberger
- Department of Forest Physiology and Genetics, Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Gabriel F Peñaloza-Bojacá
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
| | - César Plaza
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, 04510, CP, México
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Serrano 115 bis, 28006, Madrid, Spain
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Alexandra Rodríguez
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Christina Siebe
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Av. Fernando Corrêa, 2367, Boa Esperança, Cuiabá, 78060-900, MT, Brazil
| | - Alberto L Teixido
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, 80523, CO, USA
| | - Nuria Casado-Coy
- Multidisciplinary Institute for Environmental Studies (MIES), University of Alicante, P.O. Box 99, Alicante, E-03080, Spain
| | - Pankaj Trivedi
- Grupo de Biodiversidad y Cambio Global (BCG), Departamento de Ciencias. Básicas, Universidad del Bío-Bío, Campus Fernando May, Chillán, Chile
| | - Cristian Torres-Díaz
- Plant-Microbes Interaction Lab, Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Jay Prakash Verma
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Arpan Mukherjee
- Institute of Grassland Science/School of Life Science, Northeast Normal University, and Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, Jilin, China
| | - Xiao-Min Zeng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ling Wang
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, 8531100, Israel
| | - Jianyong Wang
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, 8531100, Israel
| | - Eli Zaady
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xiaobing Zhou
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan, 430000, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yong-Guan Zhu
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, E-41012, Spain
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Manuel Delgado-Baquerizo
- Unidad Asociada CSIC-UPO (BioFun)., Universidad Pablo de Olavide, Sevilla, 41013, Spain.
- CEAZA, Universidad Católica del Norte, Coquimbo, Chile.
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22
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Li X, Zhao R, Li D, Wang G, Bei S, Ju X, An R, Li L, Kuyper TW, Christie P, Bender FS, Veen C, van der Heijden MGA, van der Putten WH, Zhang F, Butterbach-Bahl K, Zhang J. Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N 2O emissions from soil. Microbiome 2023; 11:45. [PMID: 36890606 PMCID: PMC9996866 DOI: 10.1186/s40168-023-01466-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/10/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N2O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N2O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N2O emissions of isolated N2O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments. RESULTS AMF hyphae reduced denitrification-derived N2O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N2O emissions in the hyphosphere was linked to N2O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N2O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene. CONCLUSIONS The cooperation between AMF and the N2O-reducing Pseudomonas residing on hyphae significantly reduce N2O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N2O consumption in nutrient-enriched microsites, and consequently reduce N2O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.
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Affiliation(s)
- Xia Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
- College of Agronomy and Life Science, Shanxi Datong University, Datong, 037009, China
| | - Ruotong Zhao
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Dandan Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Guangzhou Wang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Shuikuan Bei
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Xiaotang Ju
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Ran An
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Long Li
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Thomas W Kuyper
- Department of Soil Quality, Wageningen University, P.O. Box 47, Wageningen, 6700 AA, The Netherlands
| | - Peter Christie
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Franz S Bender
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Ciska Veen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO KNAW), Wageningen, NL-6700 AB, The Netherlands
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
- Plant-Soil Interactions, Research Division Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO KNAW), Wageningen, NL-6700 AB, The Netherlands
| | - Fusuo Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Klaus Butterbach-Bahl
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstrasse 19, 82467, Garmisch-Partenkirchen, Germany
- Pioneer Center Land-CRAFT, Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Junling Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, China.
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23
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Abstract
The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland. .,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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24
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Alguacil MDM, Schlaeppi K, López-García Á, van der Heijden MGA, Querejeta JI. Contrasting Responses of Arbuscular Mycorrhizal Fungal Families to Simulated Climate Warming and Drying in a Semiarid Shrubland. Microb Ecol 2022; 84:941-944. [PMID: 34608508 DOI: 10.1007/s00248-021-01886-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
We carried out a 4-year manipulative field experiment in a semiarid shrubland in southeastern Spain to assess the impacts of experimental warming (W), rainfall reduction (RR), and their combination (W + RR) on the composition and diversity of arbuscular mycorrhizal fungal (AMF) communities in rhizosphere soil of H. syriacum and G. struthium shrubs using single-molecule real-time (SMRT) DNA sequencing. Across climate treatments, we encountered 109 AMF operational taxonomic units (OTUs) that were assigned to four families: Glomeraceae (93.94%), Gigasporaceae (2.19%), Claroideoglomeraceae (1.95%), and Diversisporaceae (1.92%). AMF community composition and diversity at OTU level were unaffected by the climate manipulation treatments, except for a significant decrease in AMF OTU richness in the W treatment relative to the control. However, we found a significant decrease of AMF family richness in all climate manipulation treatments relative to the control treatment. Members of the Gigasporaceae and Diversisporaceae families appeared to be highly vulnerable to intensification of heat and drought stress, as their abundances decreased by 67% and 77%, respectively, in the W + RR treatment relative to current ambient conditions. In contrast, the relative abundance and dominance of the Glomeraceae family within the AMF community increased significantly under the W + RR treatment, with Glomeraceae being the indicator family for the W + RR treatment. The interaction between warming and rainfall reduction had a significant effect on AMF community structure at family level. These findings provide new insights to help in the conservation of the soil biodiversity facing climate change in dryland ecosystems.
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Affiliation(s)
- María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain.
| | - Klaus Schlaeppi
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, The Netherlands
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - José Ignacio Querejeta
- Department of Soil and Water Conservation, CSIC-Centro de Edafología Y Biología Aplicada del Segura, Campus de Espinardo, P.O. Box 164, 30100, Murcia, Spain
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25
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Romero F, Cazzato S, Walder F, Vogelgsang S, Bender SF, van der Heijden MGA. Humidity and high temperature are important for predicting fungal disease outbreaks worldwide. New Phytol 2022; 234:1553-1556. [PMID: 33713447 DOI: 10.1111/nph.17340] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Ferran Romero
- Plant-Soil Interactions, Agroscope, Zurich, 8046, Switzerland
| | - Sabrina Cazzato
- Plant-Soil Interactions, Agroscope, Zurich, 8046, Switzerland
| | - Florian Walder
- Plant-Soil Interactions, Agroscope, Zurich, 8046, Switzerland
| | - Susanne Vogelgsang
- Ecological Plant Protection in Arable Crops, Agroscope, Zurich, 8046, Switzerland
| | - S Franz Bender
- Plant-Soil Interactions, Agroscope, Zurich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, 8057, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Agroscope, Zurich, 8046, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, 8057, Switzerland
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26
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Liu S, García-Palacios P, Tedersoo L, Guirado E, van der Heijden MGA, Wagg C, Chen D, Wang Q, Wang J, Singh BK, Delgado-Baquerizo M. Phylotype diversity within soil fungal functional groups drives ecosystem stability. Nat Ecol Evol 2022; 6:900-909. [PMID: 35534625 DOI: 10.1038/s41559-022-01756-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 12/25/2022]
Abstract
Soil fungi are fundamental to plant productivity, yet their influence on the temporal stability of global terrestrial ecosystems, and their capacity to buffer plant productivity against extreme drought events, remain uncertain. Here we combined three independent global field surveys of soil fungi with a satellite-derived temporal assessment of plant productivity, and report that phylotype richness within particular fungal functional groups drives the stability of terrestrial ecosystems. The richness of fungal decomposers was consistently and positively associated with ecosystem stability worldwide, while the opposite pattern was found for the richness of fungal plant pathogens, particularly in grasslands. We further demonstrated that the richness of soil decomposers was consistently positively linked with higher resistance of plant productivity in response to extreme drought events, while that of fungal plant pathogens showed a general negative relationship with plant productivity resilience/resistance patterns. Together, our work provides evidence supporting the critical role of soil fungal diversity to secure stable plant production over time in global ecosystems, and to buffer against extreme climate events.
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Affiliation(s)
- Shengen Liu
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China.,Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain.,Huitong Experimental Station of Forest Ecology, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Shenyang, PR China
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain.,Andalusian Center for Assessment and Monitoring of Global Change (CAESCG), University of Almeria, Almeria, Spain
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Cameron Wagg
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, Canada
| | - Dima Chen
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, China
| | - Qingkui Wang
- Huitong Experimental Station of Forest Ecology, CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Shenyang, PR China.,School of Forestry & Landscape Architecture, Anhui Agricultural University, Hefei, China
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain. .,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, Spain.
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27
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Querejeta JI, Schlaeppi K, López-García Á, Ondoño S, Prieto I, León-Sánchez L, van der Heijden MGA, Alguacil MDM. Corrigendum. New Phytol 2022; 234:1102. [PMID: 35226363 DOI: 10.1111/nph.17986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Affiliation(s)
- José Ignacio Querejeta
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Klaus Schlaeppi
- Agroscope, Plant-Soil-Interactions, Institute for Sustainability Sciences, Reckenholzstrasse 191, 8046, Zűrich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Sara Ondoño
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Iván Prieto
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Lupe León-Sánchez
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil-Interactions, Institute for Sustainability Sciences, Reckenholzstrasse 191, 8046, Zűrich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zűrich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, the Netherlands
| | - María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
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28
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Romdhane S, Spor A, Banerjee S, Breuil MC, Bru D, Chabbi A, Hallin S, van der Heijden MGA, Saghai A, Philippot L. Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity. Environ Microbiome 2022; 17:1. [PMID: 34991714 PMCID: PMC8740439 DOI: 10.1186/s40793-021-00396-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/23/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. RESULTS We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. CONCLUSIONS Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
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Affiliation(s)
- Sana Romdhane
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Aymé Spor
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Samiran Banerjee
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Biological Sciences, North Dakota State University, Fargo, 58102, USA
| | - Marie-Christine Breuil
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - David Bru
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Abad Chabbi
- ECOSYS, UMR INRAE, AgroParisTech, Thiverval-Grignon, France
- CNRS, Institute of Ecology and Environmental Sciences-Paris (iEES-Paris, UMR Sorbonne Université, CNRS, INRAE), Thiverval-Grignon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Aurélien Saghai
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laurent Philippot
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France.
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29
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Cadot S, Gfeller V, Hu L, Singh N, Sánchez‐Vallet A, Glauser G, Croll D, Erb M, van der Heijden MGA, Schlaeppi K. Soil composition and plant genotype determine benzoxazinoid-mediated plant-soil feedbacks in cereals. Plant Cell Environ 2021; 44:3502-3514. [PMID: 34505297 PMCID: PMC9292949 DOI: 10.1111/pce.14184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/02/2021] [Accepted: 07/19/2021] [Indexed: 06/02/2023]
Abstract
Plant-soil feedbacks refer to effects on plants that are mediated by soil modifications caused by the previous plant generation. Maize conditions the surrounding soil by secretion of root exudates including benzoxazinoids (BXs), a class of bioactive secondary metabolites. Previous work found that a BX-conditioned soil microbiota enhances insect resistance while reducing biomass in the next generation of maize plants. Whether these BX-mediated and microbially driven feedbacks are conserved across different soils and response species is unknown. We found the BX-feedbacks on maize growth and insect resistance conserved between two arable soils, but absent in a more fertile grassland soil, suggesting a soil-type dependence of BX feedbacks. We demonstrated that wheat also responded to BX-feedbacks. While the negative growth response to BX-conditioning was conserved in both cereals, insect resistance showed opposite patterns, with an increase in maize and a decrease in wheat. Wheat pathogen resistance was not affected. Finally and consistent with maize, we found the BX-feedbacks to be cultivar-specific. Taken together, BX-feedbacks affected cereal growth and resistance in a soil and genotype-dependent manner. Cultivar-specificity of BX-feedbacks is a key finding, as it hides the potential to optimize crops that avoid negative plant-soil feedbacks in rotations.
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Affiliation(s)
- Selma Cadot
- Division of Agroecology and EnvironmentAgroscopeZurichSwitzerland
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
| | | | - Lingfei Hu
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentZhejiang UniversityZhejiangChina
| | - Nikhil Singh
- Laboratory of Evolutionary GeneticsUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Andrea Sánchez‐Vallet
- Plant Pathology, Institute of Integrative BiologyETH ZürichZürichSwitzerland
- Centro de Biotecnología y Genómica de Plantas (CBGP)Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM)Campus de Montegancedo UPMPozuelo de Alarcón (Madrid)Spain
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical ChemistryUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary GeneticsUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Matthias Erb
- Institute of Plant SciencesUniversity of BernBernSwitzerland
| | | | - Klaus Schlaeppi
- Division of Agroecology and EnvironmentAgroscopeZurichSwitzerland
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
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30
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Saghaï A, Banjeree S, Degrune F, Edlinger A, García-Palacios P, Garland G, van der Heijden MGA, Herzog C, Maestre FT, Pescador DS, Philippot L, Rillig MC, Romdhane S, Hallin S. Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol 2021; 24:341-356. [PMID: 34796612 DOI: 10.1111/1462-2920.15830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/28/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Anna Edlinger
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gina Garland
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Soil Quality and Use Group, Agroscope, Zurich, Switzerland.,Department of Environmental System Sciences, Soil Resources Group, ETH Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain.,Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - David S Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Móstoles, Spain
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Sana Romdhane
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Querejeta JI, Schlaeppi K, López-García Á, Ondoño S, Prieto I, van der Heijden MGA, Del Mar Alguacil M. Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition. New Phytol 2021; 232:1399-1413. [PMID: 34342894 DOI: 10.1111/nph.17661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
The aboveground impacts of climate change receive extensive research attention, but climate change could also alter belowground processes such as the delicate balance between free-living fungal decomposers and nutrient-scavenging mycorrhizal fungi that can inhibit decomposition through a mechanism called the Gadgil effect. We investigated how climate change-induced reductions in plant survival, photosynthesis and productivity alter soil fungal community composition in a mixed arbuscular/ectomycorrhizal (AM/EM) semiarid shrubland exposed to experimental warming (W) and/or rainfall reduction (RR). We hypothesised that increased EM host plant mortality under a warmer and drier climate might decrease ectomycorrhizal fungal (EMF) abundance, thereby favouring the proliferation and activity of fungal saprotrophs. The relative abundance of EMF sequences decreased by 57.5% under W+RR, which was accompanied by reductions in the activity of hydrolytic enzymes involved in the acquisition of organic-bound nutrients by EMF and their host plants. W+RR thereby created an enhanced potential for soil organic matter (SOM) breakdown and nitrogen mineralisation by decomposers, as revealed by 127-190% increases in dissolved organic carbon and nitrogen, respectively, and decreasing SOM content in soil. Climate aridification impacts on vegetation can cascade belowground through shifts in fungal guild structure that alter ecosystem biogeochemistry and accelerate SOM decomposition by reducing the Gadgil effect.
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Affiliation(s)
- José Ignacio Querejeta
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Klaus Schlaeppi
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013, Bern, Switzerland
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
| | - Álvaro López-García
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
| | - Sara Ondoño
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Iván Prieto
- Department of Soil and Water Conservation (CEBAS-CSIC), CSIC-Centro de Edafología y Biología Aplicada del Segura, PO Box 164, Campus de Espinardo, 30100, Murcia, Spain
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, the Netherlands
| | - María Del Mar Alguacil
- Soil Microbiology and Symbiotic Systems Department, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, Granada, 18008, Spain
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32
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Säle V, Palenzuela J, Azcón-Aguilar C, Sánchez-Castro I, da Silva GA, Seitz B, Sieverding E, van der Heijden MGA, Oehl F. Ancient lineages of arbuscular mycorrhizal fungi provide little plant benefit. Mycorrhiza 2021; 31:559-576. [PMID: 34327560 PMCID: PMC8484173 DOI: 10.1007/s00572-021-01042-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/08/2021] [Indexed: 05/17/2023]
Abstract
Almost all land plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Individual plants usually are colonized by a wide range of phylogenetically diverse AMF species. The impact that different AMF taxa have on plant growth is only partly understood. We screened 44 AMF isolates for their effect on growth promotion and nutrient uptake of leek plants (Allium porrum), including isolates that have not been tested previously. In particular, we aimed to test weather AMF lineages with an ancient evolutionary age differ from relatively recent lineages in their effects on leek plants. The AMF isolates that were tested covered 18 species from all five AMF orders, eight families, and 13 genera. The experiment was conducted in a greenhouse. A soil-sand mixture was used as substrate for the leek plants. Plant growth response to inoculation with AMF varied from - 19 to 232% and depended on isolate, species, and family identity. Species from the ancient families Archaeosporaceae and Paraglomeraceae tended to be less beneficial, in terms of stimulation plant growth and nutrient uptake, than species of Glomeraceae, Entrophosporaceae, and Diversisporaceae, which are considered phylogenetically more recent than those ancient families. Root colonization levels also depended on AMF family. This study indicates that plant benefit in the symbiosis between plants and AMF is linked to fungal identity and phylogeny and it shows that there are large differences in effectiveness of different AMF.
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Affiliation(s)
- Verena Säle
- Plant-Soil-Interactions, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
- Vegetable-Production Extension, Agroscope, Müller-Thurgau-Strasse 29, CH-8820, Wädenswil, Switzerland.
| | - Javier Palenzuela
- Departamento de Microbiología del Suelo Y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Concepción Azcón-Aguilar
- Departamento de Microbiología del Suelo Y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008, Granada, Spain
| | - Iván Sánchez-Castro
- Departamento de Microbiología, Universidad de Granada, Campus Universitario de Fuentenueva, 18071, Granada, Spain
| | - Gladstone Alves da Silva
- Departamento de Micologia, CCB, Universidade Federal de Pernambuco, Av. da Engenharia s/n, Cidade Universitária, Recife, PE, 50740-600, Brazil
| | - Benjamin Seitz
- Plant-Soil-Interactions, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Ewald Sieverding
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg Institute), University of Hohenheim, Garbenstr. 13, 70599, Stuttgart-Hohenheim, Germany
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8057, Zürich, Switzerland
| | - Fritz Oehl
- Ecotoxicology, Agroscope, Müller-Thurgau-Strasse 29, CH-8820, Wädenswil, Switzerland
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Qiu L, Zhang Q, Zhu H, Reich PB, Banerjee S, van der Heijden MGA, Sadowsky MJ, Ishii S, Jia X, Shao M, Liu B, Jiao H, Li H, Wei X. Erosion reduces soil microbial diversity, network complexity and multifunctionality. ISME J 2021; 15:2474-2489. [PMID: 33712698 PMCID: PMC8319411 DOI: 10.1038/s41396-021-00913-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 01/31/2023]
Abstract
While soil erosion drives land degradation, the impact of erosion on soil microbial communities and multiple soil functions remains unclear. This hinders our ability to assess the true impact of erosion on soil ecosystem services and our ability to restore eroded environments. Here we examined the effect of erosion on microbial communities at two sites with contrasting soil texture and climates. Eroded plots had lower microbial network complexity, fewer microbial taxa, and fewer associations among microbial taxa, relative to non-eroded plots. Soil erosion also shifted microbial community composition, with decreased relative abundances of dominant phyla such as Proteobacteria, Bacteroidetes, and Gemmatimonadetes. In contrast, erosion led to an increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae. Changes in microbiota characteristics were strongly related with erosion-induced changes in soil multifunctionality. Together, these results demonstrate that soil erosion has a significant negative impact on soil microbial diversity and functionality.
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Affiliation(s)
- Liping Qiu
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,CAS Center for Excellence in Quaternary Science and Global Change, Xi’an, Shaanxi China ,grid.144022.10000 0004 1760 4150College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi China
| | - Qian Zhang
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN USA ,grid.12955.3a0000 0001 2264 7233College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Hansong Zhu
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi China
| | - Peter B. Reich
- grid.17635.360000000419368657Department of Forest Resources, University of Minnesota, St. Paul, MN USA ,grid.1029.a0000 0000 9939 5719Hawkesbury Institute for the Environment, Western Sydney University, Penrith South DC, NSW Australia
| | - Samiran Banerjee
- grid.261055.50000 0001 2293 4611Department of Microbiological Sciences, North Dakota State University, Fargo, ND USA
| | - Marcel G. A. van der Heijden
- grid.417771.30000 0004 4681 910XAgroscope, Department of Agroecology & Environment, Zürich, Switzerland ,grid.7400.30000 0004 1937 0650Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Michael J. Sadowsky
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN USA ,grid.17635.360000000419368657Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN USA
| | - Satoshi Ishii
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN USA ,grid.17635.360000000419368657Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN USA
| | - Xiaoxu Jia
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,grid.9227.e0000000119573309Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Mingan Shao
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,grid.9227.e0000000119573309Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Baoyuan Liu
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China
| | - Huan Jiao
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi China
| | - Haiqiang Li
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,grid.144022.10000 0004 1760 4150College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi China
| | - Xiaorong Wei
- grid.144022.10000 0004 1760 4150State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi China ,CAS Center for Excellence in Quaternary Science and Global Change, Xi’an, Shaanxi China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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Wittwer RA, Bender SF, Hartman K, Hydbom S, Lima RAA, Loaiza V, Nemecek T, Oehl F, Olsson PA, Petchey O, Prechsl UE, Schlaeppi K, Scholten T, Seitz S, Six J, van der Heijden MGA. Organic and conservation agriculture promote ecosystem multifunctionality. Sci Adv 2021; 7:eabg6995. [PMID: 34417179 PMCID: PMC8378818 DOI: 10.1126/sciadv.abg6995] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 05/22/2023]
Abstract
Ecosystems provide multiple services to humans. However, agricultural systems are usually evaluated on their productivity and economic performance, and a systematic and quantitative assessment of the multifunctionality of agroecosystems including environmental services is missing. Using a long-term farming system experiment, we evaluated and compared the agronomic, economic, and ecological performance of the most widespread arable cropping systems in Europe: organic, conservation, and conventional agriculture. We analyzed 43 agroecosystem properties and determined overall agroecosystem multifunctionality. We show that organic and conservation agriculture promoted ecosystem multifunctionality, especially by enhancing regulating and supporting services, including biodiversity preservation, soil and water quality, and climate mitigation. In contrast, conventional cropping showed reduced multifunctionality but delivered highest yield. Organic production resulted in higher economic performance, thanks to higher product prices and additional support payments. Our results demonstrate that different cropping systems provide opposing services, enforcing the productivity-environmental protection dilemma for agroecosystem functioning.
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Affiliation(s)
- Raphaël A Wittwer
- Agroscope, Research Division Agroecology and Environment, Plant-Soil-Interactions, Reckenholzstrasse 191, 8046 Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikersrasse 107, 8008 Zürich, Switzerland
| | - S Franz Bender
- Agroscope, Research Division Agroecology and Environment, Plant-Soil-Interactions, Reckenholzstrasse 191, 8046 Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikersrasse 107, 8008 Zürich, Switzerland
| | - Kyle Hartman
- Agroscope, Research Division Agroecology and Environment, Plant-Soil-Interactions, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Sofia Hydbom
- Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden
| | - Ruy A A Lima
- Agroscope, Research Division Agroecology and Environment, Plant-Soil-Interactions, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Viviana Loaiza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Thomas Nemecek
- Agroscope, Research Division Competitiveness and System Evaluation, Life Cycle Assessment, Reckenholzstrasse 191, 8046 Zürich, Switzerland
| | - Fritz Oehl
- Agroscope, Competence Division for Plants and Plant Products, Ecotoxicology, Müller-Thurgau-Strasse 29, 8820 Wädenswil, Switzerland
| | - Pål Axel Olsson
- Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden
| | - Owen Petchey
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | | | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056 Basel, Switzerland
- University of Bern, Institute of Plant Sciences, Altenbergrain 21, 3013 Bern, Switzerland
| | - Thomas Scholten
- Soil Science and Geomorphology, Institute of Geography, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Steffen Seitz
- Soil Science and Geomorphology, Institute of Geography, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Johan Six
- Department of Environmental Systems Science, ETH-Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Marcel G A van der Heijden
- Agroscope, Research Division Agroecology and Environment, Plant-Soil-Interactions, Reckenholzstrasse 191, 8046 Zürich, Switzerland.
- Department of Plant and Microbial Biology, University of Zurich, Zollikersrasse 107, 8008 Zürich, Switzerland
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35
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Cosme M, Fernández I, Declerck S, van der Heijden MGA, Pieterse CMJ. A coumarin exudation pathway mitigates arbuscular mycorrhizal incompatibility in Arabidopsis thaliana. Plant Mol Biol 2021; 106:319-334. [PMID: 33825084 DOI: 10.1007/s11103-021-01143-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Overexpression of genes involved in coumarin production and secretion can mitigate mycorrhizal incompatibility in nonhost Arabidopsis plants. The coumarin scopoletin, in particular, stimulates pre-penetration development and metabolism in mycorrhizal fungi. Although most plants can benefit from mutualistic associations with arbuscular mycorrhizal (AM) fungi, nonhost plant species such as the model Arabidopsis thaliana have acquired incompatibility. The transcriptional response of Arabidopsis to colonization by host-supported AM fungi switches from initial AM recognition to defense activation and plant growth antagonism. However, detailed functional information on incompatibility in nonhost-AM fungus interactions is largely missing. We studied interactions between host-sustained AM fungal networks of Rhizophagus irregularis and 18 Arabidopsis genotypes affected in nonhost penetration resistance, coumarin production and secretion, and defense (salicylic acid, jasmonic acid, and ethylene) and growth hormones (auxin, brassinosteroid, cytokinin, and gibberellin). We demonstrated that root-secreted coumarins can mitigate incompatibility by stimulating fungal metabolism and promoting initial steps of AM colonization. Moreover, we provide evidence that major molecular defenses in Arabidopsis do not operate as primary mechanisms of AM incompatibility nor of growth antagonism. Our study reveals that, although incompatible, nonhost plants can harbor hidden tools that promote initial steps of AM colonization. Moreover, it uncovered the coumarin scopoletin as a novel signal in the pre-penetration dialogue, with possible implications for the chemical communication in plant-mycorrhizal fungi associations.
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Affiliation(s)
- Marco Cosme
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, the Netherlands.
- Mycology, Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain, Croix du sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium.
| | - Iván Fernández
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, the Netherlands
| | - Stéphane Declerck
- Mycology, Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain, Croix du sud 2, bte L7.05.06, 1348, Louvain-la-Neuve, Belgium
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, the Netherlands
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope Reckenholz, Reckenholzstrasse 191, 8046, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8057, Zurich, Switzerland
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, the Netherlands
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Cadot S, Guan H, Bigalke M, Walser JC, Jander G, Erb M, van der Heijden MGA, Schlaeppi K. Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Microbiome 2021; 9:103. [PMID: 33962687 DOI: 10.1101/2020.05.03.075135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/15/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties. RESULTS Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments. CONCLUSIONS These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions. Video Abstract.
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Affiliation(s)
- Selma Cadot
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Hang Guan
- Institute of Geography, University of Bern, Bern, Switzerland
| | - Moritz Bigalke
- Institute of Geography, University of Bern, Bern, Switzerland
| | | | | | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Marcel G A van der Heijden
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Klaus Schlaeppi
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
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37
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Cadot S, Guan H, Bigalke M, Walser JC, Jander G, Erb M, van der Heijden MGA, Schlaeppi K. Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field. Microbiome 2021; 9:103. [PMID: 33962687 PMCID: PMC8106187 DOI: 10.1186/s40168-021-01049-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/15/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties. RESULTS Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments. CONCLUSIONS These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions. Video Abstract.
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Affiliation(s)
- Selma Cadot
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Hang Guan
- Institute of Geography, University of Bern, Bern, Switzerland
| | - Moritz Bigalke
- Institute of Geography, University of Bern, Bern, Switzerland
| | | | | | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Marcel G A van der Heijden
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Klaus Schlaeppi
- Division of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Department of Environmental Sciences, University of Basel, Bernoullistrasse 32, 4056, Basel, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
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38
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Riedo J, Wettstein FE, Rösch A, Herzog C, Banerjee S, Büchi L, Charles R, Wächter D, Martin-Laurent F, Bucheli TD, Walder F, van der Heijden MGA. Widespread Occurrence of Pesticides in Organically Managed Agricultural Soils-the Ghost of a Conventional Agricultural Past? Environ Sci Technol 2021; 55:2919-2928. [PMID: 33534554 DOI: 10.1021/acs.est.0c06405] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pesticides are applied in large quantities to agroecosystems worldwide. To date, few studies assessed the occurrence of pesticides in organically managed agricultural soils, and it is unresolved whether these pesticide residues affect soil life. We screened 100 fields under organic and conventional management with an analytical method containing 46 pesticides (16 herbicides, 8 herbicide transformation products, 17 fungicides, seven insecticides). Pesticides were found in all sites, including 40 organic fields. The number of pesticide residues was two times and the concentration nine times higher in conventional compared to organic fields. Pesticide number and concentrations significantly decreased with the duration of organic management. Even after 20 years of organic agriculture, up to 16 different pesticide residues were present. Microbial biomass and specifically the abundance of arbuscular mycorrhizal fungi, a widespread group of beneficial plant symbionts, were significantly negatively linked to the amount of pesticide residues in soil. This indicates that pesticide residues, in addition to abiotic factors such as pH, are a key factor determining microbial soil life in agroecosystems. This comprehensive study demonstrates that pesticides are a hidden reality in agricultural soils, and our results suggest that they have harmful effects on beneficial soil life.
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Affiliation(s)
- Judith Riedo
- Plant-Soil-Interactions, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Andrea Rösch
- Environmental Analytics, Agroscope, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil-Interactions, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Lucie Büchi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Raphaël Charles
- Research Institute of Organic Agriculture FiBL, Lausanne, Switzerland
| | - Daniel Wächter
- Swiss Soil Monitoring Network (NABO), Agroscope, Zurich, Switzerland
| | | | | | | | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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39
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Bodenhausen N, Deslandes-Hérold G, Waelchli J, Held A, van der Heijden MGA, Schlaeppi K. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. Mycorrhiza 2021; 31:137-148. [PMID: 33475800 PMCID: PMC7910240 DOI: 10.1007/s00572-020-01014-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/15/2020] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhiza fungi (AMF) are beneficial soil fungi that can promote the growth of their host plants. Accurate quantification of AMF in plant roots is important because the level of colonization is often indicative of the activity of these fungi. Root colonization is traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy methods are labor-intensive, and results depend on the observer. In this study, we present a relative qPCR method to quantify AMF in which we normalized the AMF qPCR signal relative to a plant gene. First, we validated the primer pair AMG1F and AM1 in silico, and we show that these primers cover most AMF species present in plant roots without amplifying host DNA. Next, we compared the relative qPCR method with traditional microscopy based on a greenhouse experiment with Petunia plants that ranged from very high to very low levels of AMF root colonization. Finally, by sequencing the qPCR amplicons with MiSeq, we experimentally confirmed that the primer pair excludes plant DNA while amplifying mostly AMF. Most importantly, our relative qPCR approach was capable of discriminating quantitative differences in AMF root colonization and it strongly correlated (Spearman Rho = 0.875) with quantifications by traditional microscopy. Finally, we provide a balanced discussion about the strengths and weaknesses of microscopy and qPCR methods. In conclusion, the tested approach of relative qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses.
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Affiliation(s)
- Natacha Bodenhausen
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Gabriel Deslandes-Hérold
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jan Waelchli
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Alain Held
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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40
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Tamburini G, Bommarco R, Wanger TC, Kremen C, van der Heijden MGA, Liebman M, Hallin S. Agricultural diversification promotes multiple ecosystem services without compromising yield. Sci Adv 2020; 6:6/45/eaba1715. [PMID: 33148637 PMCID: PMC7673676 DOI: 10.1126/sciadv.aba1715] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/18/2020] [Indexed: 05/21/2023]
Abstract
Enhancing biodiversity in cropping systems is suggested to promote ecosystem services, thereby reducing dependency on agronomic inputs while maintaining high crop yields. We assess the impact of several diversification practices in cropping systems on above- and belowground biodiversity and ecosystem services by reviewing 98 meta-analyses and performing a second-order meta-analysis based on 5160 original studies comprising 41,946 comparisons between diversified and simplified practices. Overall, diversification enhances biodiversity, pollination, pest control, nutrient cycling, soil fertility, and water regulation without compromising crop yields. Practices targeting aboveground biodiversity boosted pest control and water regulation, while those targeting belowground biodiversity enhanced nutrient cycling, soil fertility, and water regulation. Most often, diversification practices resulted in win-win support of services and crop yields. Variability in responses and occurrence of trade-offs highlight the context dependency of outcomes. Widespread adoption of diversification practices shows promise to contribute to biodiversity conservation and food security from local to global scales.
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Affiliation(s)
- Giovanni Tamburini
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
- Department of Soil, Plant and Food Sciences (DiSSPA-Entomology), University of Bari, Bari, Italy
| | - Riccardo Bommarco
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Thomas Cherico Wanger
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Agroecology, University of Göttingen, Göttingen, Germany
| | - Claire Kremen
- Department of Environmental Sciences, Policy and Management, University of California, Berkeley, USA
- Institute for Resources, Environment and Sustainability, Biodiversity Research Center and Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Research Division Agroecology and Environment, Agroscope, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Matt Liebman
- Department of Agronomy, Iowa State University, Iowa, USA
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Hartman K, van der Heijden MGA, Wittwer RA, Banerjee S, Walser JC, Schlaeppi K. Correction to: Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome 2020; 8:66. [PMID: 32418544 PMCID: PMC7232831 DOI: 10.1186/s40168-020-00855-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Kyle Hartman
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Institute for Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Raphaël A Wittwer
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Samiran Banerjee
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | | | - Klaus Schlaeppi
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
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42
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Affiliation(s)
- Samiran Banerjee
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Reckenholz, Zürich, Switzerland.
| | - Klaus Schlaeppi
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Reckenholz, Zürich, Switzerland.,Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Department of Agroecology and Environment, Agroscope, Reckenholz, Zürich, Switzerland. .,Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland.
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43
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Sendek A, Karakoç C, Wagg C, Domínguez-Begines J, do Couto GM, van der Heijden MGA, Naz AA, Lochner A, Chatzinotas A, Klotz S, Gómez-Aparicio L, Eisenhauer N. Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity. Sci Rep 2019; 9:9650. [PMID: 31273222 PMCID: PMC6609766 DOI: 10.1038/s41598-019-45702-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/07/2019] [Indexed: 01/31/2023] Open
Abstract
Droughts associated with climate change alter ecosystem functions, especially in systems characterized by low biodiversity, such as agricultural fields. Management strategies aimed at buffering climate change effects include the enhancement of intraspecific crop diversity as well as the diversity of beneficial interactions with soil biota, such as arbuscular mycorrhizal fungi (AMF). However, little is known about reciprocal relations of crop and AMF diversity under drought conditions. To explore the interactive effects of plant genotype richness and AMF richness on plant yield under ambient and drought conditions, we established fully crossed diversity gradients in experimental microcosms. We expected highest crop yield and drought tolerance at both high barley and AMF diversity. While barley richness and AMF richness altered the performance of both barley and AMF, they did not mitigate detrimental drought effects on the plant and AMF. Root biomass increased with mycorrhiza colonization rate at high AMF richness and low barley richness. AMF performance increased under higher richness of both barley and AMF. Our findings indicate that antagonistic interactions between barley and AMF may occur under drought conditions, particularly so at higher AMF richness. These results suggest that unexpected alterations of plant-soil biotic interactions could occur under climate change.
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Affiliation(s)
- Agnieszka Sendek
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany.
- Department of Geobotany and Botanical Garden, Martin Luther University of Halle-Wittenberg, Am Kirchweg 2, 06108, Halle, Germany.
| | - Canan Karakoç
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstr. 190, Zürich, CH-8057, Switzerland
- Fredericton Research and Development Center, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
| | - Jara Domínguez-Begines
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Gabriela Martucci do Couto
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Department of Agroecology and Environment, Agroscope, Reckenholzstrasse 191, 8046, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Ali Ahmad Naz
- Crop Genetics and Biotechnology Unit, Institute of Crop Science and Resource Conservation, University of Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Alfred Lochner
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
| | - Antonis Chatzinotas
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Environmental Microbiology, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Stefan Klotz
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, 06120, Halle, Germany
| | - Lorena Gómez-Aparicio
- Institute of Natural Resources and Agrobiology of Seville (IRNAS), CSIC, LINCGlobal, Avenida Reina Mercedes, 10, 41012, Sevilla, Spain
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, 04103, Leipzig, Germany
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Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J 2019; 13:1722-1736. [PMID: 30850707 PMCID: PMC6591126 DOI: 10.1038/s41396-019-0383-2] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/04/2019] [Accepted: 02/17/2019] [Indexed: 01/28/2023]
Abstract
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.
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Affiliation(s)
- Samiran Banerjee
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Florian Walder
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Lucie Büchi
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Natural Resources Institute, University of Greenwich, London, UK
| | - Marcel Meyer
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Alain Y Held
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Andreas Gattinger
- Research Institute of Organic Agriculture FiBL, 5070, Frick, Switzerland
- Justus-Liebig University Giessen, Organic Farming with focus on Sustainable Soil Use, Karl-Glöckner-Str. 21C, 35394, Giessen, Germany
| | - Thomas Keller
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Swedish University of Agricultural Sciences, Department of Soil & Environment, Box 7014, 75007, Uppsala, Sweden
| | - Raphael Charles
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Research Institute of Organic Agriculture FiBL, Jordils 3, 1001, Lausanne, Switzerland
| | - Marcel G A van der Heijden
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
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45
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Fernández I, Cosme M, Stringlis IA, Yu K, de Jonge R, van Wees SM, Pozo MJ, Pieterse CMJ, van der Heijden MGA. Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism. New Phytol 2019; 223:867-881. [PMID: 30883790 DOI: 10.1111/nph.15798] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 03/11/2019] [Indexed: 06/09/2023]
Abstract
Approximately 29% of all vascular plant species are unable to establish an arbuscular mycorrhizal (AM) symbiosis. Despite this, AM fungi (Rhizophagus spp.) are enriched in the root microbiome of the nonhost Arabidopsis thaliana, and Arabidopsis roots become colonized when AM networks nurtured by host plants are available. Here, we investigated the nonhost-AM fungus interaction by analyzing transcriptional changes in Rhizophagus, Arabidopsis and the host plant Medicago truncatula while growing in the same mycorrhizal network. In early interaction stages, Rhizophagus activated the Arabidopsis strigolactone biosynthesis genes CCD7 and CCD8, suggesting that detection of AM fungi is not completely impaired. However, in colonized Arabidopsis roots, fungal nutrient transporter genes GintPT, GintAMT2, GintMST2 and GintMST4, essential for AM symbiosis, were not activated. RNA-seq transcriptome analysis pointed to activation of costly defenses in colonized Arabidopsis roots. Moreover, Rhizophagus colonization caused a 50% reduction in shoot biomass, but also led to enhanced systemic immunity against Botrytis cinerea. This suggests that early signaling between AM fungi and Arabidopsis is not completely impaired and that incompatibility appears at later interaction stages. Moreover, Rhizophagus-mediated defenses coincide with reduced Arabidopsis growth, but also with systemic disease resistance, highlighting the multifunctional role of AM fungi in host and nonhost interactions.
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Affiliation(s)
- Iván Fernández
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Marco Cosme
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - SaskiaC M van Wees
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), Granada, 18008, Spain
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB, Utrecht, the Netherlands
- Plant-Soil-Interactions, Agroscope, Zürich, 8046, Switzerland
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46
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Dennert F, Imperiali N, Staub C, Schneider J, Laessle T, Zhang T, Wittwer R, van der Heijden MGA, Smits THM, Schlaeppi K, Keel C, Maurhofer M. Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance. FEMS Microbiol Ecol 2019; 94:4985836. [PMID: 29701793 DOI: 10.1093/femsec/fiy075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 01/29/2023] Open
Abstract
Conservation tillage and organic farming are strategies used worldwide to preserve the stability and fertility of soils. While positive effects on soil structure have been extensively reported, the effects on specific root- and soil-associated microorganisms are less known. The aim of this study was to investigate how conservation tillage and organic farming influence the frequency and activity of plant-beneficial pseudomonads. Amplicon sequencing using the 16S rRNA gene revealed that Pseudomonas is among the most abundant bacterial taxa in the root microbiome of field-grown wheat, independent of agronomical practices. However, pseudomonads carrying genes required for the biosynthesis of specific antimicrobial compounds were enriched in samples from conventionally farmed plots without tillage. In contrast, disease resistance tests indicated that soil from conventional no tillage plots is less resistant to the soilborne pathogen Pythium ultimum compared to soil from organic reduced tillage plots, which exhibited the highest resistance of all compared cropping systems. Reporter strain-based gene expression assays did not reveal any differences in Pseudomonas antimicrobial gene expression between soils from different cropping systems. Our results suggest that plant-beneficial pseudomonads can be favoured by certain soil cropping systems, but soil resistance against plant diseases is likely determined by a multitude of biotic factors in addition to Pseudomonas.
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Affiliation(s)
- Francesca Dennert
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Nicola Imperiali
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Cornelia Staub
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Jana Schneider
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
| | - Titouan Laessle
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Tao Zhang
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland.,Institute of Grassland Sciences, Northeast Normal University, Key Laboratory for Vegetation Ecology, Ministry of Education, 130024 Changchun, China
| | - Raphaël Wittwer
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | | | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland
| | - Klaus Schlaeppi
- Agroscope, Division of Agroecology and Environment, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Christoph Keel
- University of Lausanne, Department of Fundamental Microbiology, Quartier UNIL-Sorge, CH-1015 Lausanne, Switzerland
| | - Monika Maurhofer
- ETH Zürich, Plant Pathology, Institute of Integrative Biology, Universitätsstrasse 2, 8092 Zürich, Switzerland
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47
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Rillig MC, Aguilar-Trigueros CA, Camenzind T, Cavagnaro TR, Degrune F, Hohmann P, Lammel DR, Mansour I, Roy J, van der Heijden MGA, Yang G. Why farmers should manage the arbuscular mycorrhizal symbiosis. New Phytol 2019; 222:1171-1175. [PMID: 30657593 DOI: 10.1111/nph.15602] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/17/2018] [Indexed: 05/09/2023]
Affiliation(s)
- Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Carlos A Aguilar-Trigueros
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Tessa Camenzind
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Timothy R Cavagnaro
- The Waite Research Institute and The School of Wine and Agriculture, The University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), CH-5070, Frick, Switzerland
| | - Daniel R Lammel
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
- Department of Soils and Agricultural Engineering, Universidade Federal do Paraná (UFPR), 80035-050, Curitiba, Brazil
| | - India Mansour
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Julien Roy
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Plant-Soil-Interactions, Agroscope, Research Division Agroecology and Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Gaowen Yang
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, D-14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
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48
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Skinner C, Gattinger A, Krauss M, Krause HM, Mayer J, van der Heijden MGA, Mäder P. The impact of long-term organic farming on soil-derived greenhouse gas emissions. Sci Rep 2019; 9:1702. [PMID: 30737429 PMCID: PMC6368562 DOI: 10.1038/s41598-018-38207-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/19/2018] [Indexed: 01/22/2023] Open
Abstract
Agricultural practices contribute considerably to emissions of greenhouse gases. So far, knowledge on the impact of organic compared to non-organic farming on soil-derived nitrous oxide (N2O) and methane (CH4) emissions is limited. We investigated N2O and CH4 fluxes with manual chambers during 571 days in a grass-clover- silage maize - green manure cropping sequence in the long-term field trial "DOK" in Switzerland. We compared two organic farming systems - biodynamic (BIODYN) and bioorganic (BIOORG) - with two non-organic systems - solely mineral fertilisation (CONMIN) and mixed farming including farmyard manure (CONFYM) - all reflecting Swiss farming practices-together with an unfertilised control (NOFERT). We observed a 40.2% reduction of N2O emissions per hectare for organic compared to non-organic systems. In contrast to current knowledge, yield-scaled cumulated N2O emissions under silage maize were similar between organic and non-organic systems. Cumulated on area scale we recorded under silage maize a modest CH4 uptake for BIODYN and CONMIN and high CH4 emissions for CONFYM. We found that, in addition to N input, quality properties such as pH, soil organic carbon and microbial biomass significantly affected N2O emissions. This study showed that organic farming systems can be a viable measure contributing to greenhouse gas mitigation in the agricultural sector.
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Affiliation(s)
- Colin Skinner
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse, CH-5070, Frick, Switzerland
| | - Andreas Gattinger
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse, CH-5070, Frick, Switzerland. .,Organic Farming with focus on Sustainable Soil Use, Institute of Crop Science and Breeding II, Justus-Liebig University Giessen, 35394, Giessen, Germany.
| | - Maike Krauss
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse, CH-5070, Frick, Switzerland
| | - Hans-Martin Krause
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse, CH-5070, Frick, Switzerland
| | - Jochen Mayer
- Water Protection and Substance Flows, Research Division Agroecology and Environment, Agroscope, CH 8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Research Division Agroecology and Environment, Agroscope, CH 8046, Zürich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, CH 8057, Zürich, Switzerland.,Institute of Environmental Biology, Faculty of Science, Utrecht University, 3508, TC, Utrecht, The Netherlands
| | - Paul Mäder
- Department of Soil Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse, CH-5070, Frick, Switzerland
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Schweizer SA, Seitz B, van der Heijden MGA, Schulin R, Tandy S. Impact of organic and conventional farming systems on wheat grain uptake and soil bioavailability of zinc and cadmium. Sci Total Environ 2018; 639:608-616. [PMID: 29800854 DOI: 10.1016/j.scitotenv.2018.05.187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Steffen A Schweizer
- Soil Protection, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätstrasse 16, 8092 Zurich, Switzerland; Soil Science, Department of Ecology and Ecosystem Management, Technical University of Munich, Emil-Ramann-Straße 2, 85354 Freising, Germany.
| | - Benjamin Seitz
- Plant-Soil Interactions, Agroscope, Reckenholzstrasse 191, 8046 Zurich, Switzerland; Environmental Geosciences, University of Basel, Bernoullistrasse 30, 4056 Basel, Switzerland.
| | - Marcel G A van der Heijden
- Plant-Soil Interactions, Agroscope, Reckenholzstrasse 191, 8046 Zurich, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rainer Schulin
- Soil Protection, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätstrasse 16, 8092 Zurich, Switzerland.
| | - Susan Tandy
- Soil Protection, Institute of Terrestrial Ecosystems, ETH Zürich, Universitätstrasse 16, 8092 Zurich, Switzerland.
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Banerjee S, Thrall PH, Bissett A, van der Heijden MGA, Richardson AE. Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. Ecol Evol 2018; 8:8217-8230. [PMID: 30250697 PMCID: PMC6145019 DOI: 10.1002/ece3.4346] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 01/11/2023] Open
Abstract
Ecotones between distinct ecosystems have been the focus of many studies as they offer valuable insights into key drivers of community structure and ecological processes that underpin function. While previous studies have examined a wide range of above-ground parameters in ecotones, soil microbial communities have received little attention. Here we investigated spatial patterns, composition, and co-occurrences of archaea, bacteria, and fungi, and their relationships with soil ecological processes across a woodland-grassland ecotone. Geostatistical kriging and network analysis revealed that the community structure and spatial patterns of soil microbiota varied considerably between three habitat components across the ecotone. Woodland samples had significantly higher diversity of archaea while the grassland samples had significantly higher diversity of bacteria. Microbial co-occurrences reflected differences in soil properties and ecological processes. While microbial networks were dominated by bacterial nodes, different ecological processes were linked to specific microbial guilds. For example, soil phosphorus and phosphatase activity formed the largest clusters in their respective networks, and two lignolytic enzymes formed joined clusters. Bacterial ammonia oxidizers were dominant over archaeal oxidizers and showed a significant association (p < 0.001) with potential nitrification (PNR), with the PNR subnetwork being dominated by Betaproteobacteria. The top ten keystone taxa comprised six bacterial and four fungal OTUs, with Random Forest Analysis revealing soil carbon and nitrogen as the determinants of the abundance of keystone taxa. Our results highlight the importance of assessing interkingdom associations in soil microbial networks. Overall, this study shows how ecotones can be used as a model to delineate microbial structural patterns and ecological processes across adjoining land-uses within a landscape.
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Affiliation(s)
- Samiran Banerjee
- CSIRO Agriculture and FoodCanberraACTAustralia
- Agroscope, Research Division Agroecology and EnvironmentPlant‐Soil‐Interactions Group, ReckenholzZurichSwitzerland
| | | | | | - Marcel G. A. van der Heijden
- Agroscope, Research Division Agroecology and EnvironmentPlant‐Soil‐Interactions Group, ReckenholzZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZürichSwitzerland
- Institute of Environmental BiologyFaculty of ScienceUtrecht UniversityUtrechtThe Netherlands
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