1
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Mmbando GS. The link between changing in host carbon allocation and resistance to Magnaporthe oryzae: a possible tactic for mitigating the rice blast fungus. PLANT SIGNALING & BEHAVIOR 2024; 19:2326870. [PMID: 38465846 PMCID: PMC10936674 DOI: 10.1080/15592324.2024.2326870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/29/2024] [Indexed: 03/12/2024]
Abstract
One of the most destructive diseases affecting rice is rice blast, which is brought on by the rice blast fungus Magnaporthe oryzae. The preventive measures, however, are not well established. To effectively reduce the negative effects of rice blasts on crop yields, it is imperative to comprehend the dynamic interactions between pathogen resistance and patterns of host carbon allocation. This review explores the relationship between variations in carbon allocation and rice plants' ability to withstand the damaging effects of M. oryzae. The review highlights potential strategies for altering host carbon allocation including transgenic, selective breeding, crop rotation, and nutrient management practices as a promising avenue for enhancing rice blast resistance. This study advances our knowledge of the interaction between plants' carbon allocation and M. oryzae resistance and provides stakeholders and farmers with practical guidance on mitigating the adverse effects of the rice blast globally. This information may be used in the future to create varieties that are resistant to M. oryzae.
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Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma, Dodoma, Tanzania
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2
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Marques M, Sierra-Garcia IN, Leitão F, Martins J, Patinha C, Pinto G, Cunha Â. Rhizosphere-xylem sap connections in the olive tree microbiome: implications for biostimulation approaches. J Appl Microbiol 2024; 135:lxae152. [PMID: 38906841 DOI: 10.1093/jambio/lxae152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/12/2024] [Accepted: 06/20/2024] [Indexed: 06/23/2024]
Abstract
AIMS Climate change is endangering olive groves. Farmers are adapting by exploring new varieties of olive trees and examining the role of microbiomes in plant health.The main objectives of this work were to determine the primary factors that influence the microbiome of olive trees and to analyze the connection between the rhizosphere and endosphere compartments. METHODS AND RESULTS The rhizosphere and xylem sap microbiomes of two olive tree varieties were characterized by next-generation 16S rRNA amplicon sequencing, and soil descriptors were analyzed. Bacterial communities in the rhizosphere of olive trees were more diverse than those found in the xylem sap. Pseudomonadota, Actinobacteriota, Acidobacteriota, and Bacillota were the dominant phyla in both compartments. At the genus level, only very few taxa were shared between soil and sap bacterial communities. CONCLUSIONS The composition of the bacteriome was more affected by the plant compartment than by the olive cultivar or soil properties, and a direct route from the rhizosphere to the endosphere could not be confirmed. The large number of plant growth-promoting bacteria found in both compartments provides promising prospects for improving agricultural outcomes through microbiome engineering.
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Affiliation(s)
- Mónica Marques
- CESAM & Department of Biology University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
| | - I Natalia Sierra-Garcia
- CESAM & Department of Biology University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
| | - Frederico Leitão
- Department of Life Sciences, Centre for Functional Ecology, Faculty of Science and Technology, University of Coimbra, Coimbra 3000-456, Portugal
| | - João Martins
- CESAM & Department of Biology University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
- Department of Geosciences & Geobiotec, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
| | - Carla Patinha
- Department of Geosciences & Geobiotec, University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
| | - Glória Pinto
- CESAM & Department of Biology University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
| | - Ângela Cunha
- CESAM & Department of Biology University of Aveiro, Campus de Santiago, Aveiro 3810-193, Portugal
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3
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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4
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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5
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Sena L, Mica E, Valè G, Vaccino P, Pecchioni N. Exploring the potential of endophyte-plant interactions for improving crop sustainable yields in a changing climate. FRONTIERS IN PLANT SCIENCE 2024; 15:1349401. [PMID: 38571718 PMCID: PMC10988515 DOI: 10.3389/fpls.2024.1349401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Climate change poses a major threat to global food security, significantly reducing crop yields as cause of abiotic stresses, and for boosting the spread of new and old pathogens and pests. Sustainable crop management as a route to mitigation poses the challenge of recruiting an array of solutions and tools for the new aims. Among these, the deployment of positive interactions between the micro-biotic components of agroecosystems and plants can play a highly significant role, as part of the agro-ecological revolution. Endophytic microorganisms have emerged as a promising solution to tackle this challenge. Among these, Arbuscular Mycorrhizal Fungi (AMF) and endophytic bacteria and fungi have demonstrated their potential to alleviate abiotic stresses such as drought and heat stress, as well as the impacts of biotic stresses. They can enhance crop yields in a sustainable way also by other mechanisms, such as improving the nutrient uptake, or by direct effects on plant physiology. In this review we summarize and update on the main types of endophytes, we highlight several studies that demonstrate their efficacy in improving sustainable yields and explore possible avenues for implementing crop-microbiota interactions. The mechanisms underlying these interactions are highly complex and require a comprehensive understanding. For this reason, omic technologies such as genomics, transcriptomics, proteomics, and metabolomics have been employed to unravel, by a higher level of information, the complex network of interactions between plants and microorganisms. Therefore, we also discuss the various omic approaches and techniques that have been used so far to study plant-endophyte interactions.
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Affiliation(s)
- Lorenzo Sena
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Erica Mica
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Giampiero Valè
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica, UPO – Università del Piemonte Orientale, Complesso San Giuseppe, Vercelli, Italy
| | - Patrizia Vaccino
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Nicola Pecchioni
- Dipartimento di Scienze della Vita, Sede Agraria, UNIMORE - Università di Modena e Reggio Emilia, Reggio Emilia, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
- Centro di Ricerca Cerealicoltura e Colture Industriali, CREA – Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Foggia, Italy
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6
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Salse J, Barnard RL, Veneault-Fourrey C, Rouached H. Strategies for breeding crops for future environments. TRENDS IN PLANT SCIENCE 2024; 29:303-318. [PMID: 37833181 DOI: 10.1016/j.tplants.2023.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/27/2023] [Accepted: 08/08/2023] [Indexed: 10/15/2023]
Abstract
The green revolution successfully increased agricultural output in the early 1960s by relying primarily on three pillars: plant breeding, irrigation, and chemical fertilization. Today, the need to reduce the use of chemical fertilizers, water scarcity, and future environmental changes, together with a growing population, requires innovative strategies to adapt to a new context and prevent food shortages. Therefore, scientists from around the world are directing their efforts to breed crops for future environments to sustainably produce more nutritious food. Herein, we propose scientific avenues to be reinforced in selecting varieties, including crop wild relatives, either for monoculture or mixed cropping systems, taking advantage of plant-microbial interactions, while considering the diversity of organisms associated with crops and unlocking combinatorial nutritional stresses.
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Affiliation(s)
- Jérôme Salse
- UCA-INRAE UMR 1095 Genetics, Diversity, and Ecophysiology of Cereals (GDEC), 5 Chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Romain L Barnard
- Agroécologie, INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Claire Veneault-Fourrey
- Université de Lorraine, INRAE, Unité Mixte de Recherche Interactions Arbres-Microorganismes, F-54000 Nancy, France
| | - Hatem Rouached
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48823, USA.
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7
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Kimotho RN, Maina S. Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers? JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1289-1313. [PMID: 37950741 PMCID: PMC10901211 DOI: 10.1093/jxb/erad448] [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: 05/26/2023] [Accepted: 11/08/2023] [Indexed: 11/13/2023]
Abstract
Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.
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Affiliation(s)
- Roy Njoroge Kimotho
- Hebei Key Laboratory of Soil Ecology, Key Laboratory of Agricultural Water Resources, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Solomon Maina
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales 2568, Australia
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8
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Wang N, Wang X, Chen L, Liu H, Wu Y, Huang M, Fang L. Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168994. [PMID: 38043809 DOI: 10.1016/j.scitotenv.2023.168994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.
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Affiliation(s)
- Na Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, The Research Center of Soil and Water Conservation and Ecological Environment, CAS and MOE, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangxiang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Li Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Hongjie Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yanfang Wu
- Palm Eco-Town Development Co., Ltd., Zhengzhou 450000, China
| | - Min Huang
- Key Laboratory of Green Utilization of Critical Nonmetallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, The Research Center of Soil and Water Conservation and Ecological Environment, CAS and MOE, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, CAS and MWR, Yangling 712100, China; Key Laboratory of Green Utilization of Critical Nonmetallic Mineral Resources, Ministry of Education, Wuhan University of Technology, Wuhan 430070, China.
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9
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Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
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Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
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10
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Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
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Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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11
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Ramírez-Sánchez D, Gibelin-Viala C, Roux F, Vailleau F. Genetic architecture of the response of Arabidopsis thaliana to a native plant-growth-promoting bacterial strain. FRONTIERS IN PLANT SCIENCE 2023; 14:1266032. [PMID: 38023938 PMCID: PMC10665851 DOI: 10.3389/fpls.2023.1266032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
By improving plant nutrition and alleviating abiotic and biotic stresses, plant growth-promoting bacteria (PGPB) can help to develop eco-friendly and sustainable agricultural practices. Besides climatic conditions, soil conditions, and microbe-microbe interactions, the host genotype influences the effectiveness of PGPB. Yet, most GWAS conducted to characterize the genetic architecture of response to PGPB are based on non-native interactions between a host plant and PGPB strains isolated from the belowground compartment of other plants. In this study, a GWAS was set up under in vitro conditions to describe the genetic architecture of the response of Arabidopsis thaliana to the PGPB Pseudomonas siliginis, by inoculating seeds of 162 natural accessions from the southwest of France with one strain isolated from the leaf compartment in the same geographical region. Strong genetic variation of plant growth response to this native PGPB was observed at a regional scale, with the strain having a positive effect on the vegetative growth of small plants and a negative effect on the vegetative growth of large plants. The polygenic genetic architecture underlying this negative trade-off showed suggestive signatures of local adaptation. The main eco-evolutionary relevant candidate genes are involved in seed and root development.
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12
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Liu C, Jiang M, Yuan MM, Wang E, Bai Y, Crowther TW, Zhou J, Ma Z, Zhang L, Wang Y, Ding J, Liu W, Sun B, Shen R, Zhang J, Liang Y. Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils. NATURE FOOD 2023; 4:912-924. [PMID: 37783790 DOI: 10.1038/s43016-023-00848-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.
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Affiliation(s)
- Chaoyang Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Meitong Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengting Maggie Yuan
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Thomas W Crowther
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhiyuan Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Li Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jixian Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Wuxing Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Renfang Shen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.
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13
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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14
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Sikora RA, Helder J, Molendijk LPG, Desaeger J, Eves-van den Akker S, Mahlein AK. Integrated Nematode Management in a World in Transition: Constraints, Policy, Processes, and Technologies for the Future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:209-230. [PMID: 37186900 DOI: 10.1146/annurev-phyto-021622-113058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plant-parasitic nematodes are one of the most insidious pests limiting agricultural production, parasitizing mostly belowground and occasionally aboveground plant parts. They are an important and underestimated component of the estimated 30% yield loss inflicted on crops globally by biotic constraints. Nematode damage is intensified by interactions with biotic and abiotic factors constraints: soilborne pathogens, soil fertility degradation, reduced soil biodiversity, climate variability, and policies influencing the development of improved management options. This review focuses on the following topics: (a) biotic and abiotic constraints, (b) modification of production systems, (c) agricultural policies, (d) the microbiome, (e) genetic solutions, and (f) remote sensing. Improving integrated nematode management (INM) across all scales of agricultural production and along the Global North-Global South divide, where inequalities influence access to technology, is discussed. The importance of the integration of technological development in INM is critical to improving food security and human well-being in the future.
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Affiliation(s)
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | | | - Johan Desaeger
- Institute of Food and Agricultural Sciences, Department of Entomology and Nematology, Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
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15
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Li H, Song K, Zhang X, Wang D, Dong S, Liu Y, Yang L. Application of Multi-Perspectives in Tea Breeding and the Main Directions. Int J Mol Sci 2023; 24:12643. [PMID: 37628823 PMCID: PMC10454712 DOI: 10.3390/ijms241612643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Tea plants are an economically important crop and conducting research on tea breeding contributes to enhancing the yield and quality of tea leaves as well as breeding traits that satisfy the requirements of the public. This study reviews the current status of tea plants germplasm resources and their utilization, which has provided genetic material for the application of multi-omics, including genomics and transcriptomics in breeding. Various molecular markers for breeding were designed based on multi-omics, and available approaches in the direction of high yield, quality and resistance in tea plants breeding are proposed. Additionally, future breeding of tea plants based on single-cellomics, pangenomics, plant-microbe interactions and epigenetics are proposed and provided as references. This study aims to provide inspiration and guidance for advancing the development of genetic breeding in tea plants, as well as providing implications for breeding research in other crops.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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16
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Bourak K, Sare AR, Allaoui A, Jijakli MH, Massart S. Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota. Int J Mol Sci 2023; 24:9879. [PMID: 37373026 DOI: 10.3390/ijms24129879] [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: 04/21/2023] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.
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Affiliation(s)
- Kaoutar Bourak
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - Abdoul Razack Sare
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Abdelmounaaim Allaoui
- Microbiology Laboratory, African Genome Center (AGC), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
| | - M Haissam Jijakli
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
| | - Sébastien Massart
- Terra Research Center, Integrated and Urban Plant Pathology Laboratory, Liege University, Gembloux Agro-Bio-Tech, B-5030 Gembloux, Belgium
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17
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Liu Q, Cheng L, Nian H, Jin J, Lian T. Linking plant functional genes to rhizosphere microbes: a review. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:902-917. [PMID: 36271765 PMCID: PMC10106864 DOI: 10.1111/pbi.13950] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/09/2022] [Accepted: 10/16/2022] [Indexed: 05/04/2023]
Abstract
The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.
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Affiliation(s)
- Qi Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lang Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jian Jin
- Northeast Institute of Geography and AgroecologyChinese Academy of SciencesHarbinChina
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioscienceLa Trobe UniversityBundooraVictoriaAustralia
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of AgricultureSouth China Agricultural UniversityGuangzhouChina
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18
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Shade A. Microbiome rescue: directing resilience of environmental microbial communities. Curr Opin Microbiol 2023; 72:102263. [PMID: 36657335 DOI: 10.1016/j.mib.2022.102263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/30/2022] [Accepted: 12/18/2022] [Indexed: 01/18/2023]
Abstract
Earth's climate crisis threatens to disrupt ecosystem services and destabilize food security. Microbiome management will be a crucial component of a comprehensive strategy to maintain stable microbinal functions for ecosystems and plants in the face of climate change. Microbiome rescue is the directed, community-level recovery of microbial populations and functions lost after an environmental disturbance. Microbiome rescue aims to propel a resilience trajectory for community functions. Rescue can be achieved via demographic, functional, adaptive, or evolutionary recovery of disturbance-sensitive populations. Various ecological mechanisms support rescue, including dispersal, reactivation from dormancy, functional redundancy, plasticity, and diversification, and these mechanisms can interact. Notably, controlling microbial reactivation from dormancy is a potentially fruitful but underexplored target for rescue.
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Affiliation(s)
- Ashley Shade
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, École Centrale de Lyon, Ampère, UMR5005, 69134 Ecully cedex, France; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, MI 48824, USA; The Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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19
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Wang N, Scherm H. Key Discoveries in Plant Pathology During the Past Half Century: Impacts on the Life Sciences and on Plant Disease Management. PHYTOPATHOLOGY 2023; 113:588-593. [PMID: 37116465 DOI: 10.1094/phyto-02-23-0070-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plant pathology plays a critical role in safeguarding plant health, food security, and food safety through science-based solutions to protect plants against recurring and emerging diseases. In addition, plant pathology contributed significantly to basic discoveries that have had broad impacts on the life sciences beyond plant pathology. In December 2021, The American Phytopathological Society (APS) conducted a survey among its members and among the readership of its journals to identify and rank key discoveries in plant pathology that have had broad impacts on science and/or practical disease management during the past half century. Based on the responses received, key discoveries that have broadly impacted the life sciences during that period include the Agrobacterium Ti plasmid and its mechanism in T-DNA transfer, bacterial ice nucleation, cloning of resistance genes, discovery of viroids, effectors and their mechanisms, pattern-triggered immunity and effector-triggered immunity, RNA interference and gene silencing, structure and function of R genes, transcription activator-like effectors, and type-III secretion system and hrp/hrc. Major advances that significantly impacted practical disease management include the deployment and management of host resistance genes; the application of disease models and forecasting systems; the introduction of modern systemic fungicides and host resistance inducers, along with a better understanding of fungicide resistance mechanisms and management; and the utilization of biological controls and suppressive soils, including the implementation of methyl-bromide alternatives. In this special issue, experts from the pertinent fields review the discovery process, recent progress, and impacts of some of the highest ranked discoveries in each category while also pointing out future directions for new discoveries in fundamental and applied plant pathology.
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Affiliation(s)
- Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL 33850
| | - Harald Scherm
- Department of Plant Pathology, University of Georgia, Athens, GA 30605
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20
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Yang S, Liu H, Xie P, Wen T, Shen Q, Yuan J. Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4441-4449. [PMID: 36890647 DOI: 10.1021/acs.jafc.2c08758] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The increasing impacts of global climate change on crop performance pose a significant threat to global food security. The rhizosphere microbiomes intimately interact with the plant and can largely facilitate plants in growth promotion and stress resistance via multiple mechanisms. This review focuses on approaches for harnessing the rhizosphere microbiomes to produce beneficial effects toward enhanced crop productivity, including the use of organic and inorganic amendments, and microbial inoculants. Emerging methods, such as the utilization of synthetic microbial consortia, host-mediated microbiome engineering, prebiotics made from specific plant root exudates, and crop breeding to promote beneficial plant-microbiome interactions, are highlighted. Updating our knowledge in this field is critical for understanding and improving plant-microbiome interactions, thereby enhancing plant adaptiveness to changing environmental conditions.
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Affiliation(s)
- Shengdie Yang
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2753, Australia
| | - Penghao Xie
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Tao Wen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Yuan
- The Key Laboratory of Plant Immunity, Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China
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21
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Boutsika A, Michailidis M, Ganopoulou M, Dalakouras A, Skodra C, Xanthopoulou A, Stamatakis G, Samiotaki M, Tanou G, Moysiadis T, Angelis L, Bazakos C, Molassiotis A, Nianiou-Obeidat I, Mellidou I, Ganopoulos I. A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes. iScience 2023; 26:105917. [PMID: 36691616 PMCID: PMC9860355 DOI: 10.1016/j.isci.2022.105917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.
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Affiliation(s)
- Anastasia Boutsika
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University, 54124 Thessaloniki, Greece
| | - Michail Michailidis
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
| | - Maria Ganopoulou
- School of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Dalakouras
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
| | - Christina Skodra
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001 Thessaloniki-Thermi, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
| | - George Stamatakis
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming”, 16672 Vari, Greece
| | - Georgia Tanou
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, Greece
| | - Theodoros Moysiadis
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, 2417 Nicosia, Cyprus
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
- Max Planck Institute for Plant Breeding Research, Department of Comparative Development and Genetics, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, 57001 Thessaloniki-Thermi, Greece
| | - Irini Nianiou-Obeidat
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University, 54124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
- Corresponding author
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, 570001 Thessaloniki-Thermi, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, 57001 Thessaloniki-Thermi, 21 Greece
- Corresponding author
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22
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Zhang C, Shi X, Zhang J, Zhang Y, Wang W. Dynamics of soil microbiome throughout the cultivation life cycle of morel ( Morchella sextelata). Front Microbiol 2023; 14:979835. [PMID: 36910237 PMCID: PMC9992412 DOI: 10.3389/fmicb.2023.979835] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.
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Affiliation(s)
- Chen Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xiaofei Shi
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jiexiong Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yesheng Zhang
- Shandong Junsheng Biotechnologies Co., Ltd., Liaocheng, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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23
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Zhu QL, Yan K, Wang NZ, Ma SQ, Lu DS, Su XH, Yuan ZS, Dong YF, Wang YP, Ding CJ. The structure and assembly of rhizobacterial communities are influenced by poplar genotype. Front Microbiol 2022; 13:1052567. [DOI: 10.3389/fmicb.2022.1052567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3–-N content and 58 genera to NH4+-N/NO3–-N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3–-N content and fluctuated with increasing NH4+-N/NO3–-N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.
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Sun L, Dong X, Wang Y, Maker G, Agarwal M, Ding Z. Tea-Soybean Intercropping Improves Tea Quality and Nutrition Uptake by Inducing Changes of Rhizosphere Bacterial Communities. Microorganisms 2022; 10:2149. [PMID: 36363740 PMCID: PMC9697773 DOI: 10.3390/microorganisms10112149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/26/2023] Open
Abstract
The positive aspects of the tea plant/legume intercropping system draw attention to the Chinese tea industry for its benefit for soil fertility improvement with low fertilizer input. However, limited information exists as to the roles of intercropped legumes in the rhizosphere microbiome and tea quality. Hereby, soybean was selected as the intercropped plant to investigate its effect on bacterial communities, nutrient competition, tea plant development, and tea quality. Our data showed that intercropped soybean boosted the uptake of nitrogen in tea plants and enhanced the growth of young tea shoots. Nutrient competition for phosphorus and potassium in soil existed between soybeans and tea plants. Moreover, tea/soybean intercropping improved tea quality, manifested by a significantly increased content of non-ester type catechins (C, EGC, EC), total catechins and theanine, and decreased content of ester type catechins (EGCG). Significant differences in rhizobacterial composition were also observed under different systems. At the genus level, the relative abundance of beneficial bacteria, such as Bradyrhizobium, Saccharimonadales and Mycobacterium, was significantly increased with the intercropping system, while the relative abundance of denitrifying bacteria, Pseudogulbenkiania, was markedly decreased. Correlation analysis showed that Pseudogulbenkiania, SBR1031, and Burkholderiaceae clustered together showing a similar correlation with soil physicochemical and tea quality characteristics; however, other differential bacteria showed the opposite pattern. In conclusion, tea/soybean intercropping improves tea quality and nutrition uptake by increasing the relative abundance of beneficial rhizosphere bacteria and decreasing denitrifying bacteria. This study strengthens our understanding of how intercropping system regulate the soil bacterial community to maintain the health of soils in tea plantations and provides the basis for replacing chemical fertilizers and improving the ecosystem in tea plantations.
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Affiliation(s)
- Litao Sun
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth, WA 6150, Australia
| | - Xue Dong
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao 266109, China
| | - Garth Maker
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth, WA 6150, Australia
| | - Manjree Agarwal
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth, WA 6150, Australia
- Scientific Service Division, Chemcentre, Government of Western Australia, B.No. 500, Corner of Manning Road and Townsing Drive, Bentley, WA 6102, Australia
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Perth, WA 6150, Australia
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Dastogeer KMG, Kao-Kniffin J, Okazaki S. Editorial: Plant microbiome: Diversity, functions, and applications. Front Microbiol 2022; 13:1039212. [PMID: 36225380 PMCID: PMC9549354 DOI: 10.3389/fmicb.2022.1039212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Khondoker M. G. Dastogeer
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Khondoker M. G. Dastogeer
| | - Jenny Kao-Kniffin
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Shin Okazaki
- Plant Microbiology Laboratory, Tokyo University of Agriculture and Technology, Tokyo, Japan
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