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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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2
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Kakouridis A, Yuan M, Nuccio EE, Hagen JA, Fossum CA, Moore ML, Estera-Molina KY, Nico PS, Weber PK, Pett-Ridge J, Firestone MK. Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter. THE NEW PHYTOLOGIST 2024; 242:1661-1675. [PMID: 38358052 DOI: 10.1111/nph.19560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/04/2023] [Indexed: 02/16/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
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Affiliation(s)
- Anne Kakouridis
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mengting Yuan
- University of California Berkeley, Berkeley, CA, 94720, USA
| | - Erin E Nuccio
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - John A Hagen
- University of California Berkeley, Berkeley, CA, 94720, USA
| | | | - Madeline L Moore
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katerina Y Estera-Molina
- University of California Berkeley, Berkeley, CA, 94720, USA
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Peter S Nico
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, 94550, CA, USA
- University of California Merced, Merced, 95343, CA, USA
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Ding Y, Gao X, Shu D, Siddique KHM, Song X, Wu P, Li C, Zhao X. Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171332. [PMID: 38447716 DOI: 10.1016/j.scitotenv.2024.171332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.
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Affiliation(s)
- Yanhong Ding
- College of Water Resources and Architectural Engineering, Northwest A&F University, Yangling, Shannxi 712100, China; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University, Yangling, Shannxi 712100, China
| | - Xiaodong Gao
- Institute of Soil and Water Conservation, Northwest A&F University, No, 26, Xinong Road, Yangling, Shannxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, China
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture & Environment, The University of Western Australia, Perth, WA 6001, Australia
| | - Xiaolin Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pute Wu
- Institute of Soil and Water Conservation, Northwest A&F University, No, 26, Xinong Road, Yangling, Shannxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, China
| | - Changjian Li
- Institute of Soil and Water Conservation, Northwest A&F University, No, 26, Xinong Road, Yangling, Shannxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, China.
| | - Xining Zhao
- Institute of Soil and Water Conservation, Northwest A&F University, No, 26, Xinong Road, Yangling, Shannxi 712100, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, Shannxi 712100, China.
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4
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Calderon RB, Dangi SR. Arbuscular Mycorrhizal Fungi and Rhizobium Improve Nutrient Uptake and Microbial Diversity Relative to Dryland Site-Specific Soil Conditions. Microorganisms 2024; 12:667. [PMID: 38674611 PMCID: PMC11052256 DOI: 10.3390/microorganisms12040667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) and rhizobium play a significant role in plant symbiosis. However, their influence on the rhizosphere soil microbiome associated with nutrient acquisition and soil health is not well defined in the drylands of Montana (MT), USA. This study investigated the effect of microbial inoculants as seed treatment on pea yield, nutrient uptake, potential microbial functions, and rhizosphere soil microbial communities using high-throughput sequencing of 16S and ITS rRNA genes. The experiment was conducted under two contrasting dryland conditions with four treatments: control, single inoculation with AMF or Rhizobium, and dual inoculations of AMF and Rhizobium (AMF+Rhizobium). Our findings revealed that microbial inoculation efficacy was site-specific. AMF+Rhizobium synergistically increased grain yield at Sidney dryland field site (DFS) 2, while at Froid site, DFS 1, AMF improved plant resilience to acidic soil but contributed a marginal yield under non-nutrient limiting conditions. Across dryland sites, the plants' microbial dependency on AMF+Rhizobium (12%) was higher than single inoculations of AMF (8%) or Rhizobium (4%) alone. Variations in microbial community structure and composition indicate a site-specific response to AMF and AMF+Rhizobium inoculants. Overall, site-specific factors significantly influenced plant nutrient uptake, microbial community dynamics, and functional potential. It underscores the need for tailored management strategies that consider site-specific characteristics to optimize benefits from microbial inoculation.
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Affiliation(s)
- Rosalie B. Calderon
- Agricultural Research Service, Northern Plains Agricultural Research Laboratory, USDA, 1500 N Central Avenue, Sidney, MT 59270, USA
| | - Sadikshya R. Dangi
- Correspondence: (R.B.C.); (S.R.D.); Tel.: +1-(406)-433-9479 (R.B.C.); +1-(406)-433-9490 (S.R.D.); Fax: +1-(406)-433-5038 (R.B.C. & S.R.D.)
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5
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Li M, Hu J, Wei Z, Jousset A, Pommier T, Yu X, Xu Y, Shen Q. Synthetic microbial communities: Sandbox and blueprint for soil health enhancement. IMETA 2024; 3:e172. [PMID: 38868511 PMCID: PMC10989119 DOI: 10.1002/imt2.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 06/14/2024]
Abstract
We summarize here the use of SynComs in improving various dimensions of soil health, including fertility, pollutant removal, soil-borne disease suppression, and soil resilience; as well as a set of useful guidelines to assess and understand the principles for designing SynComs to enhance soil health. Finally, we discuss the next stages of SynComs applications, including highly diverse and multikingdom SynComs targeting several functions simultaneously.
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Affiliation(s)
- Mei Li
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and NutritionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Jie Hu
- Department of Microbial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic‐Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic‐Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingChina
| | - Thomas Pommier
- UMR INRAE 1418 Ecologie MicrobienneUniversité Claude Bernard Lyon 1VilleurbanneFrance
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and NutritionJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic‐Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic‐Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource‐Saving FertilizersNanjing Agricultural UniversityNanjingChina
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6
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Maurice K, Bourceret A, Youssef S, Boivin S, Laurent-Webb L, Damasio C, Boukcim H, Selosse MA, Ducousso M. Anthropic disturbances impact the soil microbial network structure and stability to a greater extent than natural disturbances in an arid ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167969. [PMID: 37914121 DOI: 10.1016/j.scitotenv.2023.167969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Growing pressure from climate change and agricultural land use is destabilizing soil microbial community interactions. Yet little is known about microbial community resistance and adaptation to disturbances over time. This hampers our ability to determine the recovery latency of microbial interactions after disturbances, with fundamental implications for ecosystem functioning and conservation measures. Here we examined the response of bacterial and fungal community networks in the rhizosphere of Haloxylon salicornicum (Moq.) Bunge ex Boiss. over the course of soil disturbances resulting from a history of different hydric constraints involving flooding-drought successions. An anthropic disturbance related to past agricultural use, with frequent successions of flooding and drought, was compared to a natural disturbance, i.e., an evaporation basin, with yearly flooding-drought successions. The anthropic disturbance resulted in a specific microbial network topology characterized by lower modularity and stability, reflecting the legacy of past agricultural use on soil microbiome. In contrast, the natural disturbance resulted in a network topology and stability close to those of natural environments despite the lower alpha diversity, and a different community composition compared to that of the other sites. These results highlighted the temporality in the response of the microbial community structure to disturbance, where long-term adaptation to flooding-drought successions lead to a higher stability than disturbances occurring over a shorter timescale.
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Affiliation(s)
- Kenji Maurice
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France.
| | - Amélia Bourceret
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Sami Youssef
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France
| | - Stéphane Boivin
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Liam Laurent-Webb
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France
| | - Coraline Damasio
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
| | - Hassan Boukcim
- Department of Research and Development, VALORHIZ, 1900, Boulevard de la Lironde, PSIII, Parc Scientifique Agropolis, F34980 Montferrier sur Lez, France; ASARI, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid Ben Guerir, 43150, Morocco
| | - Marc-André Selosse
- ISYEB, Muséum national d'Histoire naturelle, CNRS, EPHE-PSL, Sorbonne Université, 57 rue Cuvier, CP39, 75005 Paris, France; Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland; Institut Universitaire de France, Paris, France
| | - Marc Ducousso
- LSTM, Univ Montpellier, CIRAD, INRAE, IRD, SupAgro, UMR082 LSTM, 34398 Montpellier Cedex 5, France
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7
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He H, Zhou J, Wang Y, Jiao S, Qian X, Liu Y, Liu J, Chen J, Delgado-Baquerizo M, Brangarí AC, Chen L, Cui Y, Pan H, Tian R, Liang Y, Tan W, Ochoa-Hueso R, Fang L. Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers. GLOBAL CHANGE BIOLOGY 2024; 30:e17028. [PMID: 37955302 DOI: 10.1111/gcb.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.
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Affiliation(s)
- Haoran He
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxiong Zhou
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
| | - Yunqiang Wang
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xun Qian
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Ji Liu
- Hubei Province Key Laboratory for Geographical Process Analysis and Simulation, Central China Normal University, Wuhan, China
| | - Ji Chen
- State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, China
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Albert C Brangarí
- Institute for Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Haibo Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Renmao Tian
- Institute for Food Safety and Health (IFSH), Illinois Institute of Technology, Bedford Park, Illinois, USA
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Campus del Rio San Pedro, Cádiz, Spain
| | - Linchuan Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, China
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Green Utilization of Critical Non-Metallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan, China
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8
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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9
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Wang Y, Hu C, Wang X, Shi G, Lei Z, Tang Y, Zhang H, Wuriyanghan H, Zhao X. Selenium-induced rhizosphere microorganisms endow salt-sensitive soybeans with salt tolerance. ENVIRONMENTAL RESEARCH 2023; 236:116827. [PMID: 37544471 DOI: 10.1016/j.envres.2023.116827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Soil salinization is a prevalent abiotic stress that adversely affects soybean production. Rhizosphere microorganisms have been shown to modulate the rhizosphere microenvironment of plants, leading to improved stress resistance. Selenium is known to optimize the rhizosphere microbial community, however, it remains uncertain whether selenium-induced rhizosphere microorganisms can enhance plant salt tolerance. In this study, we selected two soybean varieties, including salt-tolerant and salt-sensitive, and conducted pot experiments to explore the impact of selenium application on the structure and composition of the rhizosphere microbial community of soybean plants under salt stress. Four salt-tolerant bacteria from salt-tolerant soybean rhizosphere soil fertilized with selenium under salt stress were isolated, and their effects on improving salt tolerance in salt-sensitive soybean were also investigated. Our results showed that selenium application enhanced soybean salt tolerance by optimizing the structure of the plant rhizosphere microbial community and improving soil enzyme activities in both salt-tolerant and salt-sensitive varieties. Moreover, compared with salt-only treatment, inoculation of the four bacteria led to a significant increase in the plant height (7.2%-19.8%), aboveground fresh weight (57.3%-73.5%), SPAD value (8.4%-30.3%), and K+ content (4.5%-12.1%) of salt-sensitive soybean, while reducing the content of proline (84.5%-94%), MDA (26.5%-49.3%), and Na+ (7.1%-21.3%). High-throughput sequencing of the 16 S ribosomal RNA gene indicated that the four bacteria played a crucial role in changing the community structure of salt-sensitive soybean and mitigating the effects of salt stress. This study highlighted the importance of selenium combined with beneficial microorganisms in the plant rhizosphere in alleviating salinity stress.
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Affiliation(s)
- Yin Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China; Key Laboratory of Forage and Endemic Crop Biology (Inner Mongolia University), Ministry of Education, 49 Xilinguole Road, Hohhot, 010020, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Wang
- Institute of Quality Standard and Monitoring Technology for Agro-products of Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Guangyu Shi
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Zheng Lei
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanni Tang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology (Inner Mongolia University), Ministry of Education, 49 Xilinguole Road, Hohhot, 010020, China.
| | - Xiaohu Zhao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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10
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Santos-Medellín C, Blazewicz SJ, Pett-Ridge J, Firestone MK, Emerson JB. Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nat Ecol Evol 2023; 7:1809-1822. [PMID: 37770548 DOI: 10.1038/s41559-023-02207-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.
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Affiliation(s)
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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11
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Can arbuscular mycorrhizal fungi and rhizobacteria facilitate 33P uptake in maize plants under water stress? Microbiol Res 2023; 271:127350. [PMID: 36913786 DOI: 10.1016/j.micres.2023.127350] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) are able to provide key ecosystem services, protecting plants against biotic and abiotic stresses. Here, we hypothesized that a combination of AMF (Rhizophagus clarus) and PGPR (Bacillus sp.) could enhance 33P uptake in maize plants under soil water stress. A microcosm experiment using mesh exclusion and a radiolabeled phosphorus tracer (33P) was installed using three types of inoculation: i) only AMF, ii) only PGPR, and iii) a consortium of AMF and PGPR, alongside a control treatment without inoculation. For all treatments, a gradient of three water-holding capacities (WHC) was considered i) 30% (severe drought), ii) 50% (moderate drought), and iii) 80% (optimal condition, no water stress). In severe drought conditions, AMF root colonization of dual-inoculated plants was significantly lower compared to individual inoculation of the AMF, whilst 33P uptake by dual-inoculated plants or plants inoculated with bacteria was 2.4-fold greater than the uninoculated treatment. Under moderate drought conditions the use of AMF promoted the highest 33P uptake by plants, increasing it by 2.1-fold, when compared to the uninoculated treatment. Without drought stress, AMF showed the lowest 33P uptake and, overall, plant P acquisition was lower for all inoculation types when compared to the severe and moderate drought treatments. The total shoot P content was modulated by the water-holding capacity and inoculation type, with the lowest values observed under severe drought and the highest values under moderate drought. The highest soil electrical conductivity (EC) values were found under severe drought in AMF-inoculated plants and the lowest EC for no drought in single or dual-inoculated plants. Furthermore, water-holding capacity influenced the total soil bacterial and mycorrhizal abundance over time, with the highest abundances being found under severe and moderate drought. This study demonstrates that the positive influence of microbial inoculation on 33P uptake by plants varied with soil water gradient. Furthermore, under severe stress conditions, AMF invested more in the production of hyphae, vesicles and spore production, indicating a significant carbon drain from the host plant as evidenced by the lack of translation of increased 33P uptake into biomass. Therefore, under severe drought the use of bacteria or dual-inoculation seems to be more effective than individual AMF inoculation in terms of 33P uptake by plants, while under moderate drought, the use of AMF stood out.
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12
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Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. MICROBIOME 2022; 10:199. [PMID: 36434737 PMCID: PMC9700909 DOI: 10.1186/s40168-022-01391-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. RESULTS Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera. CONCLUSIONS Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
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Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Marissa Lafler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ashley N. Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Anne Kakouridis
- Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | | | | | | | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA USA
| | | | - Mary Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA USA
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