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Chen P, Huang P, Yu H, Yu H, Xie W, Wang Y, Zhou Y, Chen L, Zhang M, Yao R. Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability. mSystems 2024; 9:e0112423. [PMID: 38780241 PMCID: PMC11237589 DOI: 10.1128/msystems.01124-23] [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: 10/20/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.
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Affiliation(s)
- Pubo Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Pingliang Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Haiyang Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Huang Yu
- School of Resource and Environment and Safety Engineering, University of South China, Hengyang, China
| | - Weicheng Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yuehua Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
| | - Yu Zhou
- Hunan Institute of Microbiology, Changsha, China
| | - Li Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Meng Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
| | - Ruifeng Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, China
- Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Yuelushan Lab, Changsha, China
- Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, China
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Chroston ECM, Bziuk N, Stauber EJ, Ravindran BM, Hielscher A, Smalla K, Wittstock U. Plant glucosinolate biosynthesis and breakdown pathways shape the rhizosphere bacterial/archaeal community. PLANT, CELL & ENVIRONMENT 2024; 47:2127-2145. [PMID: 38419355 DOI: 10.1111/pce.14870] [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: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbial community assembly results from microbe-microbe-plant interactions mediated by small molecules of plant and microbial origin. Studies with Arabidopsis thaliana have indicated a critical role of glucosinolates in shaping the root and/or rhizosphere microbial community, likely through breakdown products produced by plant or microbial myrosinases inside or outside of the root. Plant nitrile-specifier proteins (NSPs) promote the formation of nitriles at the expense of isothiocyanates upon glucosinolate hydrolysis with unknown consequences for microbial colonisation of roots and rhizosphere. Here, we generated the A. thaliana triple mutant nsp134 devoid of nitrile formation in root homogenates. Using this line and mutants lacking aliphatic or indole glucosinolate biosynthesis pathways or both, we found bacterial/archaeal alpha-diversity of the rhizosphere to be affected only by the ability to produce aliphatic glucosinolates. In contrast, bacterial/archaeal community composition depended on functional root NSPs as well as on pathways of aliphatic and indole glucosinolate biosynthesis. Effects of NSP deficiency were strikingly distinct from those of impaired glucosinolate biosynthesis. Our results demonstrate that rhizosphere microbial community assembly depends on functional pathways of both glucosinolate biosynthesis and breakdown in support of the hypothesis that glucosinolate hydrolysis by myrosinases and NSPs happens before secretion of products to the rhizosphere.
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Affiliation(s)
- Eleanor C M Chroston
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Bziuk
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Einar J Stauber
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Beena M Ravindran
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika Hielscher
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ute Wittstock
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
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Xun W, Liu Y, Ma A, Yan H, Miao Y, Shao J, Zhang N, Xu Z, Shen Q, Zhang R. Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture. THE NEW PHYTOLOGIST 2024; 242:2401-2410. [PMID: 38494698 DOI: 10.1111/nph.19697] [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: 10/13/2023] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Aiyuan Ma
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - He Yan
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Chauveau C, Roby D. Molecular complexity of quantitative immunity in plants: from QTL mapping to functional and systems biology. C R Biol 2024; 347:35-44. [PMID: 38771313 DOI: 10.5802/crbiol.153] [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: 02/16/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 05/22/2024]
Abstract
In nature, plants defend themselves against pathogen attack by activating an arsenal of defense mechanisms. During the last decades, work mainly focused on the understanding of qualitative disease resistance mediated by a few genes conferring an almost complete resistance, while quantitative disease resistance (QDR) remains poorly understood despite the fact that it represents the predominant and more durable form of resistance in natural populations and crops. Here, we review our past and present work on the dissection of the complex mechanisms underlying QDR in Arabidopsis thaliana. The strategies, main steps and challenges of our studies related to one atypical QDR gene, RKS1 (Resistance related KinaSe 1), are presented. First, from genetic analyses by QTL (Quantitative Trait Locus) mapping and GWAs (Genome Wide Association studies), the identification, cloning and functional analysis of this gene have been used as a starting point for the exploration of the multiple and coordinated pathways acting together to mount the QDR response dependent on RKS1. Identification of RKS1 protein interactors and complexes was a first step, systems biology and reconstruction of protein networks were then used to decipher the molecular roadmap to the immune responses controlled by RKS1. Finally, exploration of the potential impact of key components of the RKS1-dependent gene network on leaf microbiota offers interesting and challenging perspectives to decipher how the plant immune systems interact with the microbial communities' systems.
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Yue H, Sun X, Wang T, Zhang A, Han D, Wei G, Song W, Shu D. Host genotype-specific rhizosphere fungus enhances drought resistance in wheat. MICROBIOME 2024; 12:44. [PMID: 38433268 PMCID: PMC10910722 DOI: 10.1186/s40168-024-01770-8] [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: 08/22/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses. RESULTS Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum). CONCLUSIONS Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.
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Affiliation(s)
- Hong Yue
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xuming Sun
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Wang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ali Zhang
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dejun Han
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
| | - Weining Song
- College of Agronomy, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Duntao Shu
- College of Life Sciences, National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi, 712100, China.
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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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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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10
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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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11
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Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1276472. [PMID: 38023837 PMCID: PMC10663345 DOI: 10.3389/fpls.2023.1276472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.
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Affiliation(s)
| | - Feng Huang
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Center for Genomics and Systems Biology, Department of Biology, College of Arts and Science, New York University, New York, NY, United States
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12
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Tian Y, Liu Y, Uwaremwe C, Zhao X, Yue L, Zhou Q, Wang Y, Tran LSP, Li W, Chen G, Sha Y, Wang R. Characterization of three new plant growth-promoting microbes and effects of the interkingdom interactions on plant growth and disease prevention. PLANT CELL REPORTS 2023; 42:1757-1776. [PMID: 37674059 DOI: 10.1007/s00299-023-03060-3] [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: 06/04/2023] [Accepted: 08/12/2023] [Indexed: 09/08/2023]
Abstract
KEY MESSAGE The novel interkingdom PGPM consortia enhanced the ability of plant growth promotion and disease resistance, which would be beneficial to improve plant growth in sustainable agriculture through engineering microbiome. Plant growth-promoting microbes (PGPMs) play important roles in promoting plant growth and bio-controlling of pathogens. Much information reveals that the plant growth-promoting ability of individual PGPM affects plant growth. However, the effects of the PGPM consortia properties on plant growth remain largely unexplored. Here, we characterized three new PGPM strains including Rhodotorula graminis JJ10.1 (termed as J), Pseudomonas psychrotolerans YY7 (termed as Y) and P. chlororaphis T8 (termed as T), and assessed their effects in combination with Bacillus amyloliquefaciens FZB42 (termed as F) on plant growth promotion and disease prevention in Arabidopsis thaliana and tomato (Solanum lycopersicum) plants by investigating morphological changes, whole-genome sequencing and plant growth promoting (PGP) characterization. Results revealed that the three new strains R. graminis JJ10.1, P. psychrotolerans YY7 and P. chlororaphis T8 had the potential for being combined with B. amyloliquefaciens FZB42 to form interkingdom PGPM consortia. The combinations of R. graminis JJ10.1, B. amyloliquefaciens FZB42, and P. psychrotolerans YY7, i. e. JF and JYF, exhibited the strongest ability of synergetic biofilm production. Furthermore, the growth-promotion abilities of the consortia were significantly enhanced compared with those of individual strains under both inoculation and volatile organic compounds (VOCs) treatment. Importantly, the consortia showed stronger abilities of in planta disease prevention than individual strains. Findings of our study may provide future guidance for engineering the minimal microbiome communities to improve plant growth and/or disease resistance in sustainable agriculture.
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Affiliation(s)
- Yuan Tian
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yang Liu
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Constantine Uwaremwe
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xia Zhao
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Liang Yue
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qin Zhou
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China
| | - Lam-Son Phan Tran
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Weiqiang Li
- Jilin Da'an Agro-Ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Science, Changchun, 130102, People's Republic of China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin, 730900, People's Republic of China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, People's Republic of China
| | - Ruoyu Wang
- Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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13
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Wang M, Cernava T. Soterobionts: disease-preventing microorganisms and proposed strategies to facilitate their discovery. Curr Opin Microbiol 2023; 75:102349. [PMID: 37369150 DOI: 10.1016/j.mib.2023.102349] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Crop production and the food security that it provides are currently threatened worldwide by plant pathogens. Conventional control measures, such as breeding for resistant plants, are progressively losing their efficacy due to rapidly evolving pathogens. The plant microbiota contributes to essential functions of host plants, among which is protection against pathogens. Only recently, microorganisms that provide holistic protection against certain plant diseases were identified. They were termed as 'soterobionts' and extend their host's immune system, which results in disease-resistant phenotypes. Further exploration of such microorganisms could not only provide answers to better understand the implications of the plant microbiota in health and disease, but also contribute to new developments in agriculture and beyond. The aim of this work is to point out how the identification of plant-associated soterobionts can be facilitated, and to discuss technologies that will be required to enable this.
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Affiliation(s)
- Mengcen Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China; Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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14
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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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15
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Guo Q, Zhu Y, Korpelainen H, Niinemets Ü, Li C. How does plant sex alter microbiota assembly in dioecious plants? Trends Microbiol 2023; 31:894-902. [PMID: 37120361 DOI: 10.1016/j.tim.2023.03.014] [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: 02/11/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 05/01/2023]
Abstract
Plant microbiota can greatly impact plant growth, defense, and health in different environments. Thus, it might be evolutionarily beneficial for plants to be able to control processes related to microbiota assembly. Dioecious plant species display sexual dimorphism in morphology, physiology, and immunity. These differences imply that male and female individuals might differently regulate their microbiota, but the role of sex in microbiota assembly has been largely neglected so far. Here, we introduce the mechanism of how sex controls microbiota in plants analogically to the sex regulation of gut microbiota in animals, in particular in humans. We argue that plant sex imposes selective pressure on filtering and constructing microbiota in the rhizosphere, phyllosphere, and endosphere along the soil-plant continuum. Since male plants are more resistant than female plants to environmental stresses, we suggest that a male host forms more stable and resistant plant microbiota that cooperate more effectively with the host to resist stresses. Male and female plants can distinguish whether a plant is of the same or different sex, and males can alleviate stress-caused damage in females. The impact of a male host on microbiota would protect female plants from unfavorable environments.
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Affiliation(s)
- Qingxue Guo
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuanjing Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Helena Korpelainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, FI-00014, Finland
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
| | - Chunyang Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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16
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Berrios L, Yeam J, Holm L, Robinson W, Pellitier PT, Chin ML, Henkel TW, Peay KG. Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth. Curr Biol 2023:S0960-9822(23)00760-1. [PMID: 37369208 DOI: 10.1016/j.cub.2023.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Bacteria, ectomycorrhizal (EcM) fungi, and land plants have been coevolving for nearly 200 million years, and their interactions presumably contribute to the function of terrestrial ecosystems. The direction, stability, and strength of bacteria-EcM fungi interactions across landscapes and across a single plant host, however, remains unclear. Moreover, the genetic mechanisms that govern them have not been addressed. To these ends, we collected soil samples from Bishop pine forests across a climate-latitude gradient spanning coastal California, fractionated the soil samples based on their proximity to EcM-colonized roots, characterized the microbial communities using amplicon sequencing, and generated linear regression models showing the impact that select bacterial taxa have on EcM fungal abundance. In addition, we paired greenhouse experiments with transcriptomic analyses to determine the directionality of these relationships and identify which genes EcM-synergist bacteria express during tripartite symbioses. Our data reveal that ectomycorrhizas (i.e., EcM-colonized roots) enrich conserved bacterial taxa across climatically heterogeneous regions. We also show that phylogenetically diverse EcM synergists are positively associated with plant and fungal growth and have unique gene expression profiles compared with EcM-antagonist bacteria. In sum, we identify common mechanisms that facilitate widespread and diverse multipartite symbioses, which inform our understanding of how plants develop in complex environments.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jay Yeam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wallis Robinson
- Forestry and Forest Health Program, University of California Cooperative Extension Humboldt and Del Norte Counties, Eureka, CA 95503, USA
| | | | - Mei Lin Chin
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
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17
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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Addison S, Armstrong C, Wigley K, Hartley R, Wakelin S. What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata. ENVIRONMENTAL MICROBIOME 2023; 18:45. [PMID: 37254222 DOI: 10.1186/s40793-023-00507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p < 0.005). Bacterial and fungal phyllosphere microbiome richness was lowest in samples from the top of the canopy, subsequently increasing in the middle and then bottom canopy samples. These differences maybe driven by either by (1) exchange of microbiomes with the forest floor and soil with the lower foliage, (2) strong ecological filtering in the upper canopy via environmental exposure (e.g., UV), (3) canopy density, (4) or combinations of factors. Most taxa present in the top canopy were also present lower in tree; as such, sampling strategies focussing on lower canopy sampling should provide good overall phyllosphere microbiome coverage for the tree. The dominant phyllosphere bacteria were Alpha-proteobacteria (Rhizobiales and Sphingomonas) along with Acidobacteria Gp1. However, the P. radiata phyllosphere microbiome samples were fungal dominated. From the top canopy samples, Arthoniomycetes and Dothideomycetes were highly represented, with abundances of Arthoniomycetes then reducing in lower canopy samples whilst abundances of Ascomycota increased. The most abundant fungal taxa were Phaeococcomyces (14.4% of total reads) and Phaeotheca spp. (10.38%). A second-order effect of canopy sampling direction was evident in bacterial community composition (p = 0.01); these directional influences were not evident for fungal communities. However, sterilisation of needles did impact fungal community composition (p = 0.025), indicating potential for community differences in the endosphere versus leaf surface compartments. Needle age was only important in relation to bacterial communities, but was canopy height dependant (interaction p = 0.008). By building an understanding of the primary and secondary factors related to intra-canopy phyllosphere microbiome variation, we provide a sampling framework to either explicitly minimise or capture variation in needle collection to enable ongoing ecological studies targeted at inter-canopy or other experimental levels.
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Affiliation(s)
| | | | | | | | - Steven Wakelin
- Scion, P.O. Box 29237, Riccarton, Christchurch, 8440, New Zealand.
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Escudero Martinez CM. Plant-microbe interactions: Mining heritable root-associated microbiota across environments. Curr Biol 2023; 33:R413-R415. [PMID: 37220735 DOI: 10.1016/j.cub.2023.03.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The root-associated microbiota represents an untapped reservoir of beneficial functions for plants. A new study begins unravelling the host genetic determinants governing these interactions across environments, which will be a key step towards the development of novel climate-smart crops.
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20
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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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21
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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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22
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Zhang J, Liu W, Bu J, Lin Y, Bai Y. Host genetics regulate the plant microbiome. Curr Opin Microbiol 2023; 72:102268. [PMID: 36708613 DOI: 10.1016/j.mib.2023.102268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weidong Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jingshu Bu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
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23
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Karlström A, Papp-Rupar M, Passey TAJ, Deakin G, Xu X. Quantitative trait loci associated with apple endophytes during pathogen infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1054914. [PMID: 37056502 PMCID: PMC10086318 DOI: 10.3389/fpls.2023.1054914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
The plant phyllosphere is colonized by microbial communities that can influence the fitness and growth of their host, including the host's resilience to plant pathogens.There are multiple factors involved in shaping the assemblages of bacterial and fungal endophytes within the phyllosphere, including host genetics and environment. In this work, the role of host genetics in plant-microbiome assembly was studied in a full-sibling family of apple (Malus x domestica) trees infected with the fungal pathogen Neonectria ditissima. A Quantitative Trait Loci (QTL) analysis showed that there are multiple loci which influence the abundance of individual endophytic taxa, with the majority of QTL having a moderate to large effect (20-40%) on endophyte abundance. QTL regions on LG 1, 3, 4, 5, 10, 12, 13, 14 and 15 were shown to affect multiple taxa. Only a small proportion of the variation in overall taxonomic composition was affected by host genotype, with significant QTL hits for principal components explaining <8% and <7.4% of the total variance in bacterial and fungal composition, respectively. Four of the identified QTL colocalised with previously identified regions associated with tolerance to Neonectria ditissima. These results suggest that there is a genetic basis shaping apple endophyte composition and that microbe-host associations in apple could be tailored through breeding.
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24
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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25
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DeWolf E, Brock MT, Calder WJ, Kliebenstein DJ, Katz E, Li B, Morrison HG, Maïgnien L, Weinig C. The rhizosphere microbiome and host plant glucosinolates exhibit feedback cycles in Brassica rapa. Mol Ecol 2023; 32:741-751. [PMID: 36373270 DOI: 10.1111/mec.16782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
The rhizosphere microbiome influences many aspects of plant fitness, including production of secondary compounds and defence against insect herbivores. Plants also modulate the composition of the microbial community in the rhizosphere via secretion of root exudates. We tested both the effect of the rhizosphere microbiome on plant traits, and host plant effects on rhizosphere microbes using recombinant inbred lines (RILs) of Brassica rapa that differ in production of glucosinolates (GLS), secondary metabolites that contribute to defence against insect herbivores. First, we investigated the effect of genetic variation in GLS production on the composition of the rhizosphere microbiome. Using a Bayesian Dirichlet-multinomial regression model (DMBVS), we identified both negative and positive associations between bacteria from six genera and the concentration of five GLS compounds produced in plant roots. Additionally, we tested the effects of microbial inoculation (an intact vs. disrupted soil microbiome) on GLS production and insect damage in these RILs. We found a significant microbial treatment × genotype interaction, in which total GLS was higher in the intact relative to the disrupted microbiome treatment in some RILs. However, despite differences in GLS production between microbial treatments, we observed no difference in insect damage between treatments. Together, these results provide evidence for a full feedback cycle of plant-microbe interactions mediated by GLS; that is, GLS compounds produced by the host plant "feed-down" to influence rhizosphere microbial community and rhizosphere microbes "feed-up" to influence GLS production.
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Affiliation(s)
- Ella DeWolf
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | | | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Ella Katz
- Department of Plant Sciences, University of California Davis, Davis, California, USA
| | - Baohua Li
- Department of Plant Sciences, University of California Davis, Davis, California, USA.,College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hilary G Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Lois Maïgnien
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA.,Laboratory of Microbiology of Extreme Environments, UMR 6197, Institut Européen de la Mer, Université de Bretagne Occidentale, Plouzane, France
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, USA
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26
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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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27
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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28
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Li K, Cheng K, Wang H, Zhang Q, Yang Y, Jin Y, He X, Wu R. Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:996121. [PMID: 36275601 PMCID: PMC9583167 DOI: 10.3389/fpls.2022.996121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few have systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions - mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140-728 SNPs (Single nucleotide polymorphisms) responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22-43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the "endophenotype" role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.
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Affiliation(s)
- Kaihang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kexin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haochen Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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29
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Profile of Joy M. Bergelson. Proc Natl Acad Sci U S A 2022; 119:e2212768119. [PMID: 35994635 PMCID: PMC9436368 DOI: 10.1073/pnas.2212768119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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