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Qiu P, Zheng B, Yuan H, Yang Z, Lindsey K, Wang Y, Ming Y, Zhang L, Hu Q, Shaban M, Kong J, Zhang X, Zhu L. The elicitor VP2 from Verticillium dahliae triggers defence response in cotton. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:497-511. [PMID: 37883523 PMCID: PMC10826990 DOI: 10.1111/pbi.14201] [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: 06/15/2023] [Revised: 08/25/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023]
Abstract
Verticillium dahliae is a widespread and destructive soilborne vascular pathogenic fungus that causes serious diseases in dicot plants. Here, comparative transcriptome analysis showed that the number of genes upregulated in defoliating pathotype V991 was significantly higher than in the non-defoliating pathotype 1cd3-2 during the early response of cotton. Combined with analysis of the secretome during the V991-cotton interaction, an elicitor VP2 was identified, which was highly upregulated at the early stage of V991 invasion, but was barely expressed during the 1cd3-2-cotton interaction. Full-length VP2 could induce cell death in several plant species, and which was dependent on NbBAK1 but not on NbSOBIR1 in N. benthamiana. Knock-out of VP2 attenuated the pathogenicity of V991. Furthermore, overexpression of VP2 in cotton enhanced resistance to V. dahliae without causing abnormal plant growth and development. Several genes involved in JA, SA and lignin synthesis were significantly upregulated in VP2-overexpressing cotton. The contents of JA, SA, and lignin were also significantly higher than in the wild-type control. In summary, the identified elicitor VP2, recognized by the receptor in the plant membrane, triggers the cotton immune response and enhances disease resistance.
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Affiliation(s)
- Ping Qiu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Baoxin Zheng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Hang Yuan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Zhaoguang Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | | | - Yan Wang
- College of Plant Protection, Nanjing Agricultural UniversityNanjingPeople's Republic of China
| | - Yuqing Ming
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Lin Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Qin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Department of Plant Breeding and GeneticsUniversity of Agriculture FaisalabadFaisalabadPakistan
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural SciencesUrumqiPeople's Republic of China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanPeople's Republic of China
- Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanPeople's Republic of China
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [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: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Aqueel R, Badar A, Roy N, Mushtaq Q, Ali AF, Bashir A, Ijaz UZ, Malik KA. Cotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum. NPJ Biofilms Microbiomes 2023; 9:100. [PMID: 38097579 PMCID: PMC10721634 DOI: 10.1038/s41522-023-00470-9] [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: 08/09/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
The failure of breeding strategies has caused scientists to shift to other means where the new approach involves exploring the microbiome to modulate plant defense mechanisms against Cotton Leaf Curl Disease (CLCuD). The cotton microbiome of CLCuD-resistant varieties may harbor a multitude of bacterial genera that significantly contribute to disease resistance and provide information on metabolic pathways that differ between the susceptible and resistant varieties. The current study explores the microbiome of CLCuD-susceptible Gossypium hirsutum and CLCuD-resistant Gossypium arboreum using 16 S rRNA gene amplification for the leaf endophyte, leaf epiphyte, rhizosphere, and root endophyte of the two cotton species. This revealed that Pseudomonas inhabited the rhizosphere while Bacillus was predominantly found in the phyllosphere of CLCuV-resistant G. arboreum. Using salicylic acid-producing Serratia spp. and Fictibacillus spp. isolated from CLCuD-resistant G. arboreum, and guided by our analyses, we have successfully suppressed CLCuD in the susceptible G. hirsutum through pot assays. The applied strains exhibited less than 10% CLCuD incidence as compared to control group where it was 40% at 40 days post viral inoculation. Through detailed analytics, we have successfully demonstrated that the applied microbes serve as a biocontrol agent to suppress viral disease in Cotton.
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Affiliation(s)
- Rhea Aqueel
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, G11 6EW, UK
| | - Ayesha Badar
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Nazish Roy
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Qandeel Mushtaq
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Aimen Fatima Ali
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Aftab Bashir
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan
| | - Umer Zeeshan Ijaz
- Water & Environment Research Group, University of Glasgow, Mazumdar-Shaw Advanced Research Centre, Glasgow, G11 6EW, UK.
- National University of Ireland, Galway, University Road, Galway, H91 TK33, Ireland.
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, L69 7BE, UK.
| | - Kauser Abdulla Malik
- Kauser Abdulla Malik School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore, 54600, Pakistan.
- Pakistan Academy of Sciences, Islamabad, Pakistan.
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Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Talbi N, Fokkens L, Audran C, Petit‐Houdenot Y, Pouzet C, Blaise F, Gay EJ, Rouxel T, Balesdent M, Rep M, Fudal I. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes. MOLECULAR PLANT PATHOLOGY 2023; 24:914-931. [PMID: 37128172 PMCID: PMC10346447 DOI: 10.1111/mpp.13338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/22/2023] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
Fungal effectors (small-secreted proteins) have long been considered as species or even subpopulation-specific. The increasing availability of high-quality fungal genomes and annotations has allowed the identification of trans-species or trans-genera families of effectors. Two avirulence effectors, AvrLm10A and AvrLm10B, of Leptosphaeria maculans, the fungus causing stem canker of oilseed rape, are members of such a large family of effectors. AvrLm10A and AvrLm10B are neighbouring genes, organized in divergent transcriptional orientation. Sequence searches within the L. maculans genome showed that AvrLm10A/AvrLm10B belong to a multigene family comprising five pairs of genes with a similar tail-to-tail organization. The two genes, in a pair, always had the same expression pattern and two expression profiles were distinguished, associated with the biotrophic colonization of cotyledons and/or petioles and stems. Of the two protein pairs further investigated, AvrLm10A_like1/AvrLm10B_like1 and AvrLm10A_like2/AvrLm10B_like2, the second one had the ability to physically interact, similarly to what was previously described for the AvrLm10A/AvrLm10B pair, and cross-interactions were also detected for two pairs. AvrLm10A homologues were identified in more than 30 Dothideomycete and Sordariomycete plant-pathogenic fungi. One of them, SIX5, is an effector from Fusarium oxysporum f. sp. lycopersici physically interacting with the avirulence effector Avr2. We found that AvrLm10A/SIX5 homologues were associated with at least eight distinct putative effector families, suggesting that AvrLm10A/SIX5 is able to cooperate with different effectors. These results point to a general role of the AvrLm10A/SIX5 proteins as "cooperating proteins", able to interact with diverse families of effectors whose encoding gene is co-regulated with the neighbouring AvrLm10A homologue.
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Affiliation(s)
- Nacera Talbi
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | - Like Fokkens
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
- Present address:
Laboratory of PhytopathologyWageningen University and ResearchWageningenNetherlands
| | - Corinne Audran
- UMR LIPMEUniversité de Toulouse, INRAE, CNRSCastanet‐TolosanFrance
| | | | - Cécile Pouzet
- FRAIB‐TRI Imaging Platform Facilities, FR AIBUniversité de Toulouse, CNRSCastanet‐TolosanFrance
| | | | - Elise J. Gay
- BIOGER, INRAEUniversité Paris‐SaclayPalaiseauFrance
| | | | | | - Martijn Rep
- Molecular Plant PathologyUniversity of AmsterdamAmsterdamNetherlands
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [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: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Affiliation(s)
- Shabana Hoosein
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Lena Neuenkamp
- Institute of Landscape Ecology, Münster University, Münster, Germany
- Department of Ecology and Multidisciplinary Institute for Environment Studies “Ramon Margalef,” University of Alicante, Alicante, Spain
| | - Pankaj Trivedi
- Microbiome Network, Department of Agricultural Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Mark W. Paschke
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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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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Li S, Wang Z, Gao M, Li T, Cui X, Zu J, Sang S, Fan W, Zhang H. Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype. BIOLOGY 2023; 12:biology12030476. [PMID: 36979167 PMCID: PMC10045276 DOI: 10.3390/biology12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Didymella arachidicola is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts (Arachis hypogaea L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of D. arachidicola remain to be revealed. In the present study, we collected 41 D. arachidicola isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in D. arachidicola. The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of D. arachidicola isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of D. arachidicola.
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Affiliation(s)
- Shaojian Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Tong Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Xiaowei Cui
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Junhuai Zu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Suling Sang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Wanwan Fan
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Haiyan Zhang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
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Zhang X, Ma YN, Wang X, Liao K, He S, Zhao X, Guo H, Zhao D, Wei HL. Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes. MICROBIOME 2022; 10:216. [PMID: 36482381 PMCID: PMC9733015 DOI: 10.1186/s40168-022-01422-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored. RESULTS To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae. CONCLUSION Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes. Video Abstract.
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Affiliation(s)
- Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yi-Nan Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xing Wang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kaiji Liao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shanwen He
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xia Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hebao Guo
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dongfang Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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10
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Lin Q, Xu Z, Li M, Wang Y, Li L. Spatial differences in Casuarina equisetifolia L. endophyte community structure. ANN MICROBIOL 2022. [DOI: 10.1186/s13213-022-01685-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
Casuarina equisetifolia, a fast-growing, abundant tree species on the southeastern coast of China, plays an important role in protecting the coastal environment, but the ecological processes that govern microbiome assembly and within-plant microorganism transmission are poorly known.
Methods
In this paper, we used ITS and 16S amplification techniques to study the diversity of fungal and bacterial endophytes in critical plant parts of this species: seeds, branchlets, and roots. Additionally, we examined the litter of this species to understand the process of branchlets from birth to litter.
Result
We uncovered a non-random distribution of endophyte diversity in which branchlets had the greatest and seeds had the lowest endophytic fungal diversity. In contrast, litter endophytic bacteria had the highest diversity, and branchlets had the lowest diversity. As for fungi, a large part of the seed microbiome was transmitted to the phyllosphere, while a large part of the bacterial microbiome in the seed was transmitted to the root.
Conclusion
Our study provides comprehensive evidence on diversity, potential sources, and transmission pathways for non-crop microbiome assembly and has implications for the management and manipulation of the non-crop microbiome in the future.
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11
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Zhang Z, Chai X, Gao Y, Zhang B, Lu Y, Du Y, Zhang Y, Ding Y, Tariq A, Ullah A, Li X, Zeng F. Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages. Microorganisms 2022; 10:microorganisms10122376. [PMID: 36557629 PMCID: PMC9785364 DOI: 10.3390/microorganisms10122376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- Correspondence: (Z.Z.); (F.Z.)
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yi Du
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Ya Ding
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.Z.); (F.Z.)
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12
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont. Int J Mol Sci 2022; 23:ijms232112952. [PMID: 36361736 PMCID: PMC9655247 DOI: 10.3390/ijms232112952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/26/2022] Open
Abstract
How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria–Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.
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Lin Q, Wang Y, Li M, Xu Z, Li L. Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L. FRONTIERS IN PLANT SCIENCE 2022; 13:988485. [PMID: 36340378 PMCID: PMC9632346 DOI: 10.3389/fpls.2022.988485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.
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15
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Zhang M, Peng C, Sun W, Dong R, Hao J. Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.). Microorganisms 2022; 10:microorganisms10102023. [PMID: 36296299 PMCID: PMC9610643 DOI: 10.3390/microorganisms10102023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.
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16
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Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
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Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
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17
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Yang H, Yang Z, Wang QC, Wang YL, Hu HW, He JZ, Zheng Y, Yang Y. Compartment and Plant Identity Shape Tree Mycobiome in a Subtropical Forest. Microbiol Spectr 2022; 10:e0134722. [PMID: 35863008 PMCID: PMC9430249 DOI: 10.1128/spectrum.01347-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/26/2022] [Indexed: 11/20/2022] Open
Abstract
Deciphering the relationships between microbes and their host plants is critical for a better understanding of microbial diversity maintenance and community stability. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a subtropical common-garden experiment. The results showed that fungal community structures significantly differed across compartments (leaf, root, and soil) and different tree species. Higher α-diversity was observed in the phyllosphere than in the roots and rhizospheric soil. Fungal community composition (β-diversity) was significantly affected by both compartment and species identity. The fungal community compositions were significantly correlated with soil pH in the roots and the soils as well as with soil nitrate and leaf total phosphorus in the leaves. We found that fungal community assemblies were mainly driven by deterministic processes, regardless of compartments. Moreover, host preference analyses indicated that stronger plant/fungus preferences occurred in leaves than in roots and soils. Our results highlight the differences in tree mycobiome between aboveground and belowground compartments and have important implications for the promotion of biodiversity conservation and management sustainability for the subtropical forest. IMPORTANCE Subtropical mountain forests are widely distributed in Southern China and are characterized by high biodiversity. The interactions between plants and fungi play pivotal roles in biodiversity maintenance and community stability. Nevertheless, knowledge of fungal diversity and of the community assembly patterns of woody plants is scarce. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a common-garden experiment. We found that both compartment and plant identity influenced fungal diversity, community, and guild compositions, while deterministic processes mainly governed the fungal community assembly, especially in the rhizospheric fungal communities. Our results demonstrate that tree leaves represent stronger host/fungi preferences than do roots and soils. Together, our findings enhance the understanding of the roles of compartment and plant identity in structuring fungal communities as well as promote fungal diversity maintenance in subtropical mountain forest ecosystems.
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Affiliation(s)
- Hao Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Zhijie Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
| | - Quan-Cheng Wang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Yong-Long Wang
- Faculty of Biological Science and Technology, Baotou Teacher’s College, Baotou, Inner Mongolia, China
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
| | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Yusheng Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022; 18:e1010664. [PMID: 35793393 PMCID: PMC9292093 DOI: 10.1371/journal.ppat.1010664] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/18/2022] [Accepted: 06/10/2022] [Indexed: 12/31/2022] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3. An efficient strategy to control fungal diseases in the field is genetic control using resistant crop cultivars. Crop resistance mainly relies on gene-for-gene relationships between plant resistance (R) genes and pathogen avirulence (AVR) genes, as defined by Flor in the 1940s. However, such gene-for-gene relationships can increase in complexity over the course of plant-pathogen co-evolution. Resistance against the plant-pathogenic fungus Leptosphaeria maculans by Brassica napus and other Brassica species relies on the recognition of effector (AVR) proteins by R proteins; however, L. maculans produces an effector that suppresses a subset of these specific resistances. Using a protein structure approach, we revealed structural analogy between several of the resistance-triggering effectors, the resistance-suppressing effector, and effectors from other plant-pathogenic species in the Dothideomycetes and Sordariomycetes classes, defining a new family of effectors called LARS. Notably, cross-species expression of one LARS effector from Fulvia fulva, a pathogen of tomato, in L. maculans resulted in recognition by resistant cultivars of oilseed rape. These results highlight the need to integrate knowledge on effector structures to improve resistance management and to develop broad-spectrum resistances for multi-pathogen control of diseases.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
- * E-mail: (HVT); (IF)
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
- * E-mail: (HVT); (IF)
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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20
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Lazar N, Mesarich CH, Petit-Houdenot Y, Talbi N, Li de la Sierra-Gallay I, Zélie E, Blondeau K, Gracy J, Ollivier B, Blaise F, Rouxel T, Balesdent MH, Idnurm A, van Tilbeurgh H, Fudal I. A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLoS Pathog 2022. [PMID: 35793393 DOI: 10.1101/2020.12.17.423041v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Recognition of a pathogen avirulence (AVR) effector protein by a cognate plant resistance (R) protein triggers a set of immune responses that render the plant resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) by different mechanisms including the deletion or loss-of-function mutation of the AVR gene, the incorporation of point mutations that allow recognition to be evaded while maintaining virulence function, and the acquisition of new effectors that suppress AVR recognition. The Dothideomycete Leptosphaeria maculans, causal agent of oilseed rape stem canker, is one of the few fungal pathogens where suppression of ETI by an AVR effector has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- and Rlm9-mediated resistance triggered by AvrLm3 and AvrLm5-9, respectively. The presence of AvrLm4-7 does not impede AvrLm3 and AvrLm5-9 expression, and the three AVR proteins do not appear to physically interact. To decipher the epistatic interaction between these L. maculans AVR effectors, we determined the crystal structure of AvrLm5-9 and obtained a 3D model of AvrLm3, based on the crystal structure of Ecp11-1, a homologous AVR effector candidate from Fulvia fulva. Despite a lack of sequence similarity, AvrLm5-9 and AvrLm3 are structural analogues of AvrLm4-7 (structure previously characterized). Structure-informed sequence database searches identified a larger number of putative structural analogues among L. maculans effector candidates, including the AVR effector AvrLmS-Lep2, all produced during the early stages of oilseed rape infection, as well as among effector candidates from other phytopathogenic fungi. These structural analogues are named LARS (for Leptosphaeria AviRulence and Suppressing) effectors. Remarkably, transformants of L. maculans expressing one of these structural analogues, Ecp11-1, triggered oilseed rape immunity in several genotypes carrying Rlm3. Furthermore, this resistance could be suppressed by AvrLm4-7. These results suggest that Ecp11-1 shares a common activity with AvrLm3 within the host plant which is detected by Rlm3, or that the Ecp11-1 structure is sufficiently close to that of AvrLm3 to be recognized by Rlm3.
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Affiliation(s)
- Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | | | - Nacera Talbi
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Emilie Zélie
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Karine Blondeau
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Jérôme Gracy
- CNRS UMR 5048, INSERM U1054, Centre de Biochimie Structurale, Université Montpellier, Montpellier, France
| | | | - Françoise Blaise
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | | | - Alexander Idnurm
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
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21
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Pan S, Zhang W, Li Y, Zhou P, Zhang H, Niu L, Wang L. Understanding the ecological processes governing hydrophyte-associated bacterial communities involved in hydrophyte growth and development. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 312:114952. [PMID: 35339791 DOI: 10.1016/j.jenvman.2022.114952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Maintaining hydrophyte growth has been a major focus of aquatic ecological research. The hydrophyte microbiome plays a key role in the growth and health of hydrophytes, but the ecological processes regulating the assembly and function of hydrophyte microbial communities remain unclear. This knowledge gap limits the efficacy of managing microbiomes to enhance the capacity of hydrophytes to restore the aquatic environment. Here, we sampled three typical hydrophytes (Ceratophyllum demersum, Nymphoides peltatum, and Potamogeton crispus) to study the ecological process governing hydrophyte-associated bacterial communities. The results demonstrated that hydrophyte-associated bacterial communities were affected more by the hydrophyte host species (HEEI = 2.40) than by the environment (HEEI = 1.00). The hydrophyte host species not only affected bacterial community assembly, but reduced the diversity and network complexity of the bacterial community relative to that of the environment. Furthermore, the core taxa of two hydrophytes were identified. Chryseobacterium was the core taxon of N. peltatum, and Burkholderia-Caballeronia-Paraburkholderia, Pseudolabrys, and Pajaroellobacter were the core taxa of P. crispus. The core taxa of P. crispus were closely related to potential denitrification-related functions of bacteria and revealed that P. crispus played a role in denitrification during aquatic ecological restoration. Overall, the results of this study highlight the need to develop approaches employing hydrophyte-associated bacteria to promote the development of hydrophytes, which will be essential for increasing the utility of hydrophyte microbiomes in the future and enhancing aquatic ecological restoration.
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Affiliation(s)
- Shenyang Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Pengcheng Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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22
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Efficacy of Blackleg Major Resistance Genes in B. napus in Germany. Pathogens 2022; 11:pathogens11040461. [PMID: 35456136 PMCID: PMC9030727 DOI: 10.3390/pathogens11040461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
Leptosphaeria maculans is one of the major pathogens of oilseed rape (B. napus). It causes blackleg disease, which accounts for significant yield losses worldwide. Using cultivars that harbor major resistance (R) genes is one of the most effective control methods. However, the efficacy of major R genes is related to the frequency of the corresponding avirulence (Avr) genes in a L. maculans population. In this paper, we report the Avr profiles of L. maculans populations and the ratio of its mating types in Northern and Central regions of Germany. Eleven Avr genes in five-hundred and seventy-four isolates were characterized either by applying cotyledon tests on a B. napus differential set or by amplifying avirulence gene-specific PCR markers. Fifty-two races were determined, among which the most dominant race was Avrlm6, -7, -11, AvrlepR1, -R2. Results showed that the resistance gene Rlm2 is 100% ineffective, some other major R genes such as Rlm1, Rlm3, Rlm4 and LepR3 are partially effective (with corresponding Avr frequencies ≤ 42%), while LepR1, LepR2, Rlm6, Rlm11 and Rlm7 can still provide relatively effective resistance in the German fields investigated (with corresponding Avr frequencies of 63–100%). Sexual reproduction is a factor that enhances the potential of L. maculans to evolve under selection pressure. Mating types of the L. maculans populations did not deviate from the ratio of 1:1 in the examined regions, indicating that sexual reproduction and ascospores play central roles in the L. maculans lifecycle. Overall, this study provides an important dataset for the establishment of a strategic plan to preserve the efficacies of major R genes in Germany by applying cultivar rotations of oilseed rape.
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23
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Yu C, Diao Y, Lu Q, Zhao J, Cui S, Xiong X, Lu A, Zhang X, Liu H. Comparative Genomics Reveals Evolutionary Traits, Mating Strategies, and Pathogenicity-Related Genes Variation of Botryosphaeriaceae. Front Microbiol 2022; 13:800981. [PMID: 35283828 PMCID: PMC8905617 DOI: 10.3389/fmicb.2022.800981] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Botryosphaeriaceae, as a major family of the largest class of kingdom fungi Dothideomycetes, encompasses phytopathogens, saprobes, and endophytes. Many members of this family are opportunistic phytopathogens with a wide host range and worldwide geographical distribution, and can infect many economically important plants, including food crops and raw material plants for biofuel production. To date, however, little is known about the family evolutionary characterization, mating strategies, and pathogenicity-related genes variation from a comparative genome perspective. Here, we conducted a large-scale whole-genome comparison of 271 Dothideomycetes, including 19 species in Botryosphaeriaceae. The comparative genome analysis provided a clear classification of Botryosphaeriaceae in Dothideomycetes and indicated that the evolution of lifestyle within Dothideomycetes underwent four major transitions from non-phytopathogenic to phytopathogenic. Mating strategies analysis demonstrated that at least 3 transitions were found within Botryosphaeriaceae from heterothallism to homothallism. Additionally, pathogenicity-related genes contents in different genera varied greatly, indicative of genus-lineage expansion within Botryosphaeriaceae. These findings shed new light on evolutionary traits, mating strategies and pathogenicity-related genes variation of Botryosphaeriaceae.
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Affiliation(s)
- Chengming Yu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Yufei Diao
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Quan Lu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jiaping Zhao
- Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, China
| | - Shengnan Cui
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xiong Xiong
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Anna Lu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xingyao Zhang
- Institute of Forestry New Technology, Chinese Academy of Forestry, Beijing, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
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24
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Tamminen M, Spaak J, Tlili A, Eggen R, Stamm C, Räsänen K. Wastewater constituents impact biofilm microbial community in receiving streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:151080. [PMID: 34678363 DOI: 10.1016/j.scitotenv.2021.151080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 05/27/2023]
Abstract
Microbial life in natural biofilms is dominated by prokaryotes and microscopic eukaryotes living in dense association. In stream ecosystems, microbial biofilms influence primary production, elemental cycles, food web interactions as well as water quality. Understanding how biofilm communities respond to anthropogenic impacts, such as wastewater treatment plant (WWTP) effluent, is important given the key role of biofilms in stream ecosystem function. Here, we implemented 16S and 18S rRNA gene sequencing of stream biofilms upstream (US) and downstream (DS) of WWTP effluents in four Swiss streams to test how bacterial and eukaryotic communities respond to wastewater constituents. Stream biofilm composition was strongly affected by geographic location - particularly for bacteria. However, the abundance of certain microbial community members was related to micropollutants in the wastewater - among bacteria, micropollutant-associated members were found e.g. in Alphaproteobacteria, and among eukaryotes e.g. in Bacillariophyta (algal diatoms). This study corroborates several previously characterized responses (e.g. as seen in diatoms), but also reveals previously unknown community responses - such as seen in Alphaproteobacteria. This study advances our understanding of the ecological impact of the current wastewater treatment practices and provides information about potential new marker organisms to assess ecological change in stream biofilms.
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Affiliation(s)
- Manu Tamminen
- Department of Biology, University of Turku, Finland.
| | - Jenny Spaak
- Department of Environmental Microbiology, Eawag, Switzerland
| | - Ahmed Tlili
- Department of Environmental Toxicology, Eawag, Switzerland
| | - Rik Eggen
- Department of Environmental Toxicology, Eawag, Switzerland; Department of Environmental Systems Science, ETH Zürich, Switzerland
| | | | - Katja Räsänen
- Department of Aquatic Ecology, Eawag, Switzerland; Dept. of Biology and Environmental Science, University of Jyväskylä, Finland
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25
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Köberl M, Kusstatscher P, Wicaksono WA, Mpiira S, Kalyango F, Staver C, Berg G. Increased Yield and High Resilience of Microbiota Representatives With Organic Soil Amendments in Smallholder Farms of Uganda. FRONTIERS IN PLANT SCIENCE 2022; 12:815377. [PMID: 35185962 PMCID: PMC8847376 DOI: 10.3389/fpls.2021.815377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Organic matter inputs positively affect soil fertility and quality but management effects on the soil and plant microbiome are less understood. Therefore, we studied the response of microbial colonization of the East African highland banana cultivar "Mpologoma" (AAA genome) under different mulch and manure treatments on three representative smallholder farms in Uganda. In general, the gammaproteobacterial community appeared stable with no significant response to organic matter inputs after 24 months of treatment. Significant differences (p < 0.05) in the plant-associated carpo-, phyllo-, and rhizosphere microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. Gammaproteobacterial beta diversity was shaped by the microenvironment (44%) as well as the sampling site (4%). Global effects of treatments in the rhizosphere analyzed using linear discriminant analysis effect size showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. As shown in previous works, bunch size and total yield were highly increased with manure and mulch, however, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Samuel Mpiira
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | - Francis Kalyango
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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26
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Ma H, Xie C, Zheng S, Li P, Cheema HN, Gong J, Xiang Z, Liu J, Qin J. Potato tillage method is associated with soil microbial communities, soil chemical properties, and potato yield. J Microbiol 2022; 60:156-166. [DOI: 10.1007/s12275-022-1060-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 09/06/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022]
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Defense Strategies: The Role of Transcription Factors in Tomato-Pathogen Interaction. BIOLOGY 2022; 11:biology11020235. [PMID: 35205101 PMCID: PMC8869667 DOI: 10.3390/biology11020235] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 01/21/2023]
Abstract
Simple Summary Tomato is one of the most cultivated and economically important vegetable crops throughout the world. It is affected by a panoply of different pathogens that cause infectious diseases that reduce tomato yield and affect product quality, with the most common symptoms being wilts, leaf spots/blights, fruit spots, and rots. To survive, tomato, as other plants, have developed elaborate defense mechanisms against plant pathogens. Among several genes already identified in tomato response to pathogens, we highlight those encoding the transcription factors (TFs). TFs are regulators of gene expression and are involved in large-scale biological phenomena. Here, we present an overview of recent studies of tomato TFs regarding defense responses to pathogen attack, selected for their abundance, importance, and availability of functionally well-characterized members. Tomato TFs’ roles and the possibilities related to their use for genetic engineering in view of crop breeding are presented. Abstract Tomato, one of the most cultivated and economically important vegetable crops throughout the world, is affected by a panoply of different pathogens that reduce yield and affect product quality. The study of tomato–pathogen system arises as an ideal system for better understanding the molecular mechanisms underlying disease resistance, offering an opportunity of improving yield and quality of the products. Among several genes already identified in tomato response to pathogens, we highlight those encoding the transcription factors (TFs). TFs act as transcriptional activators or repressors of gene expression and are involved in large-scale biological phenomena. They are key regulators of central components of plant innate immune system and basal defense in diverse biological processes, including defense responses to pathogens. Here, we present an overview of recent studies of tomato TFs regarding defense responses to biotic stresses. Hence, we focus on different families of TFs, selected for their abundance, importance, and availability of functionally well-characterized members in response to pathogen attack. Tomato TFs’ roles and possibilities related to their use for engineering pathogen resistance in tomato are presented. With this review, we intend to provide new insights into the regulation of tomato defense mechanisms against invading pathogens in view of plant breeding.
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28
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Harnessing phytomicrobiome signals for phytopathogenic stress management. J Biosci 2022. [DOI: 10.1007/s12038-021-00240-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Xu G, Zhang L, Liu X, Guan F, Xu Y, Yue H, Huang JQ, Chen J, Wu N, Tian J. Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. BMC Genomics 2022; 23:37. [PMID: 34996356 PMCID: PMC8742384 DOI: 10.1186/s12864-021-08260-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/13/2021] [Indexed: 12/22/2022] Open
Abstract
Background Advances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex soil microbial communities and exploit them for plant disease management. However, soil is a complex conglomerate, which makes functional metagenomics studies very challenging. Results Metagenomes were assembled by long-read (PacBio, PB), short-read (Illumina, IL), and mixture of PB and IL (PI) sequencing of soil DNA samples were compared. Ortholog analyses and functional annotation revealed that the PI approach significantly increased the contig length of the metagenomic sequences compared to IL and enlarged the gene pool compared to PB. The PI approach also offered comparable or higher species abundance than either PB or IL alone, and showed significant advantages for studying natural product biosynthetic genes in the soil microbiomes. Conclusion Our results provide an effective strategy for combining long and short-read DNA sequencing data to explore and distill the maximum information out of soil metagenomics. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08260-3.
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Affiliation(s)
- Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Haitao Yue
- Department of Biology and Biotechnology, Xinjiang University, 666 Shengli Road, Urumqi, 830046, People's Republic of China
| | - Jin-Qun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Jieyin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
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30
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Li D, Chu Z, Zeng Z, Sima M, Huang M, Zheng B. Effects of design parameters, microbial community and nitrogen removal on the field-scale multi-pond constructed wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:148989. [PMID: 34351277 DOI: 10.1016/j.scitotenv.2021.148989] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Ecological multi-pond constructed wetlands (CWs) are an alternative wastewater treatment technology for nitrogen removal from non-point source pollution. As an important component of nitrogen cycles in the field-scale CWs, microorganisms are affected by design parameters. Nevertheless, the mechanism of design parameters affecting the distribution of microbial community and removal performance remains largely unexplored. In this study, satisfactory nitrogen removal performance was obtained in three multi-pond CWs. The highest mass removal rate per square meter (1104.0 mg/m2/day) and mass removal rate per cubic meter (590.2 mg/m3/day) for total nitrogen removal were obtained in the XY CW system during the wet season. The changes in seasonal parameters accounted for different removal performances and distributions of the microbial community. The combination of wastewater treatment technologies in the XY CW system consisting of ponds, CWs, and eco-floating treatment wetlands enriched the abundances of nitrogen-related functional genera. Correlation network analysis further demonstrated that longer hydraulic residence time and higher nitrogen concentration could intensify the enrichment of nitrogen-related functional genera. Regulating the combination of wastewater treatment technologies, the nitrogen concentration of influent, hydraulic loading rate, and water depth might promote the accumulation of microbial communities and enhance nitrogen removal. Macroscopical spatial/temporal regulation were proposed to enhance the treatment of non-point source pollution. The clarification of driving mechanism on design parameters, microbial community, and removal performance provided a novel perspective on the long-term maintenance of purification performance, practically sustainable applications, and scientific management of field-scale multi-pond CWs.
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Affiliation(s)
- Dan Li
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Zhaosheng Chu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Zhenzhong Zeng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Matthew Sima
- Department of Civil and Environmental Engineering, Princeton University, NJ 08540, USA
| | - Minsheng Huang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Binghui Zheng
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Wu C, Wang F, Zhang H, Chen G, Deng Y, Chen J, Yang J, Ge T. Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars. Appl Microbiol Biotechnol 2021; 105:9371-9383. [PMID: 34767052 DOI: 10.1007/s00253-021-11666-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.
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Affiliation(s)
- Chuanfa Wu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Fangyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Haoqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Guixian Chen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.,School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, China
| | - Yangwu Deng
- School of Resources and Environmental Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Tida Ge
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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32
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The assembly of wheat-associated fungal community differs across growth stages. Appl Microbiol Biotechnol 2021; 105:7427-7438. [PMID: 34505913 DOI: 10.1007/s00253-021-11550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 02/04/2023]
Abstract
Plant-associated fungal communities play a vital role in plant adaptations, physiological functions, and productivity. Therefore, it is important to reveal the mechanisms driving the assembly of these communities. Yet it is still not fully understood how community assembly and structure differentiate in plant compartments, growth seasons, and varieties at large geographic distances. In this study, we analyzed bulk soil and plant-associated fungal communities of five wheat varieties across two growth stages in three biogeographic sites with distances of about 324, 534, or 800 km apart between any two locations. Our results indicated that the fungal community varied primarily across the sample types (leaf endosphere, root endosphere, rhizosphere, and bulk soil), followed by growth stage. Compared with the regreening stage, lower α-diversity and more dominance by abundant species in the fungal community were observed in wheat-associated compartments (four sample types except for bulk soil) at the heading stage. Additionally, within each wheat-associated compartment across every growth stage, location had stronger effects on fungal community assembly than the wheat variety. The effects of variety on fungal community assembly were location specific as were the growth-stage patterns of varietal effects on leaf endosphere and rhizosphere fungal communities. We further detected a less diverse but abundant core fungal taxa that could be grouped into three clusters associated mainly with location. This study characterized the interplay effects between plant selection (compartment, growth stage, variety) and environment (location) on wheat-associated mycobiomes by determining drivers of fungal community assembly and core fungal taxa in field conditions. KEY POINTS: • Fungal community assembly was mainly shaped by sample type and growth stage • A lower diversity and more abundant core fungal taxa were shown at heading stage • Location had stronger effects on fungal community assembly than variety.
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Xiong C, Singh BK, He JZ, Han YL, Li PP, Wan LH, Meng GZ, Liu SY, Wang JT, Wu CF, Ge AH, Zhang LM. Plant developmental stage drives the differentiation in ecological role of the maize microbiome. MICROBIOME 2021; 9:171. [PMID: 34389047 PMCID: PMC8364065 DOI: 10.1186/s40168-021-01118-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/21/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. RESULTS Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. CONCLUSIONS Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yan-Lai Han
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Li-Hua Wan
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, Qujing, 655000, China
| | - Guo-Zhong Meng
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, Qujing, 655000, China
| | - Si-Yi Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Endophytic Microbiome Responses to Sulfur Availability in Beta vulgaris (L.). Int J Mol Sci 2021; 22:ijms22137184. [PMID: 34281236 PMCID: PMC8269133 DOI: 10.3390/ijms22137184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/20/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfur is an essential plant macronutrient, and its adequate supply allows an efficient root storage and sugar extractability in sugar beets (Beta vulgaris L.). In this study, we investigated the effect of changes in sulfur availability on the endophytic community structure of sugar beets. Plants were hydroponically grown in a complete nutrient solution (S-supplied), a nutrient solution without MgSO4 (S-deprived), and a nutrient solution without MgSO4 for six days and resupplied with 100 μM MgSO4 for 48 h (S-resupplied). The sulfur status was monitored by inductively coupled plasma ICP–OES, and combustion analysis together with the evaluation of microRNA395 as a biomarker for sulfate status. Metabarcoding of the bacterial 16S rRNA gene was carried out in order to determine leaf endophytic community structure. The Shannon diversity index significantly differed (p < 0.05) between sulfate-supplied and sulfate-deprived seedlings. Validation by Real-Time PCR showed a significant increase (p < 0.05) of Burkholderia spp. in sulfate-deprived plants as compared to sulfate-supplied ones. The study sheds new light on the effects of nutrient deficiency on the microbiome of sugar beet plants.
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Pivato B, Semblat A, Guégan T, Jacquiod S, Martin J, Deau F, Moutier N, Lecomte C, Burstin J, Lemanceau P. Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping. Front Microbiol 2021; 12:674556. [PMID: 34127925 PMCID: PMC8195745 DOI: 10.3389/fmicb.2021.674556] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.
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Affiliation(s)
- Barbara Pivato
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Amélie Semblat
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Thibault Guégan
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Samuel Jacquiod
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | | | - Florence Deau
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Nathalie Moutier
- IGEPP, INRAE, Institut Agro Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - Christophe Lecomte
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France
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36
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de Vries S, de Vries J, Archibald JM, Slamovits CH. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol Ecol 2021; 96:5904760. [PMID: 32918444 PMCID: PMC7585586 DOI: 10.1093/femsec/fiaa184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them with (i) 22 oomycete genomes and (ii) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify a S. sapeloensis-specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. Salisapilia sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany.,Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany.,Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.,Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2 Canada
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37
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Choi K, Khan R, Lee SW. Dissection of plant microbiota and plant-microbiome interactions. J Microbiol 2021; 59:281-291. [PMID: 33624265 DOI: 10.1007/s12275-021-0619-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/17/2022]
Abstract
Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.
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Affiliation(s)
- Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, 49315, Republic of Korea
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, 49315, Republic of Korea.
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38
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Fagorzi C, Bacci G, Huang R, Cangioli L, Checcucci A, Fini M, Perrin E, Natali C, diCenzo GC, Mengoni A. Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems 2021. [PMID: 33436514 DOI: 10.1101/2020.06.15.152710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.
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Affiliation(s)
- Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Rui Huang
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Lisa Cangioli
- Department of Biology, University of Florence, Florence, Italy
| | - Alice Checcucci
- Department of Biology, University of Florence, Florence, Italy
| | - Margherita Fini
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Perrin
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Natali
- Department of Biology, University of Florence, Florence, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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39
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Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis. mSystems 2021; 6:6/1/e00974-20. [PMID: 33436514 PMCID: PMC7901481 DOI: 10.1128/msystems.00974-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.
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40
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Insights into the early stages of plant-endophytic bacteria interaction. World J Microbiol Biotechnol 2021; 37:13. [PMID: 33392741 DOI: 10.1007/s11274-020-02966-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
Abstract
The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.
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Xiong C, Zhu YG, Wang JT, Singh B, Han LL, Shen JP, Li PP, Wang GB, Wu CF, Ge AH, Zhang LM, He JZ. Host selection shapes crop microbiome assembly and network complexity. THE NEW PHYTOLOGIST 2021; 229:1091-1104. [PMID: 32852792 DOI: 10.1111/nph.16890] [Citation(s) in RCA: 225] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/13/2020] [Indexed: 05/20/2023]
Abstract
Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Brajesh Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Gui-Bao Wang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, 655000, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle. J Fungi (Basel) 2020; 6:jof6040255. [PMID: 33138048 PMCID: PMC7712071 DOI: 10.3390/jof6040255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 01/19/2023] Open
Abstract
The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusariumfujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.
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Bradshaw DJ, Dickens NJ, Trefry JH, McCarthy PJ. Defining the sediment prokaryotic communities of the Indian River Lagoon, FL, USA, an Estuary of National Significance. PLoS One 2020; 15:e0236305. [PMID: 33105476 PMCID: PMC7588086 DOI: 10.1371/journal.pone.0236305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
The Indian River Lagoon, located on the east coast of Florida, USA, is an Estuary of National Significance and an important economic and ecological resource. The Indian River Lagoon faces several environmental pressures, including freshwater discharges through the St. Lucie Estuary; accumulation of anoxic, fine-grained, organic-rich sediment; and metal contamination from agriculture and marinas. Although the Indian River Lagoon has been well-studied, little is known about its microbial communities; thus, a two-year 16S amplicon sequencing study was conducted to assess the spatiotemporal changes of the sediment bacterial and archaeal groups. In general, the Indian River Lagoon exhibited a prokaryotic community that was consistent with other estuarine studies. Statistically different communities were found between the Indian River Lagoon and St. Lucie Estuary due to changes in porewater salinity causing microbes that require salts for growth to be higher in the Indian River Lagoon. The St. Lucie Estuary exhibited more obvious prokaryotic seasonality, such as a higher relative abundance of Betaproteobacteriales in wet season and a higher relative abundance of Flavobacteriales in dry season samples. Distance-based linear models revealed these communities were more affected by changes in total organic matter and copper than changes in temperature. Anaerobic prokaryotes, such as Campylobacterales, were more associated with high total organic matter and copper samples while aerobic prokaryotes, such as Nitrosopumilales, were more associated with low total organic matter and copper samples. This initial study fills the knowledge gap on the Indian River Lagoon bacterial and archaeal communities and serves as important data for future studies to compare to determine possible future changes due to human impacts or environmental changes.
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Affiliation(s)
- David J. Bradshaw
- Department of Biological Sciences, Harbor Branch Oceanographic Institute at Florida Atlantic University, Fort Pierce, FL, United States of America
| | - Nicholas J. Dickens
- Department of Biological Sciences, Harbor Branch Oceanographic Institute at Florida Atlantic University, Fort Pierce, FL, United States of America
| | - John H. Trefry
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States of America
| | - Peter J. McCarthy
- Department of Biological Sciences, Harbor Branch Oceanographic Institute at Florida Atlantic University, Fort Pierce, FL, United States of America
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Plant-Growth-Promoting Bacteria Mitigating Soil Salinity Stress in Plants. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10207326] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Soil deterioration has led to problems with the nutrition of the world’s population. As one of the most serious stressors, soil salinization has a negative effect on the quantity and quality of agricultural production, drawing attention to the need for environmentally friendly technologies to overcome the adverse effects. The use of plant-growth-promoting bacteria (PGPB) can be a key factor in reducing salinity stress in plants as they are already introduced in practice. Plants having halotolerant PGPB in their root surroundings improve in diverse morphological, physiological, and biochemical aspects due to their multiple plant-growth-promoting traits. These beneficial effects are related to the excretion of bacterial phytohormones and modulation of their expression, improvement of the availability of soil nutrients, and the release of organic compounds that modify plant rhizosphere and function as signaling molecules, thus contributing to the plant’s salinity tolerance. This review aims to elucidate mechanisms by which PGPB are able to increase plant tolerance under soil salinity.
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Xiong C, He JZ, Singh BK, Zhu YG, Wang JT, Li PP, Zhang QB, Han LL, Shen JP, Ge AH, Wu CF, Zhang LM. Rare taxa maintain the stability of crop mycobiomes and ecosystem functions. Environ Microbiol 2020; 23:1907-1924. [PMID: 32996254 DOI: 10.1111/1462-2920.15262] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/27/2020] [Indexed: 12/24/2022]
Abstract
Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant-mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil-plant continuums (rhizosphere, phyllosphere and endosphere) in the maize-wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop-associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub-community is mainly determined by stochastic processes. In contrast, the rare sub-community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co-occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qin-Bing Zhang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan, 655000, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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46
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Wang X, Cui Y, Zhang X, Ju W, Duan C, Wang Y, Fang L. A novel extracellular enzyme stoichiometry method to evaluate soil heavy metal contamination: Evidence derived from microbial metabolic limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139709. [PMID: 32590116 DOI: 10.1016/j.scitotenv.2020.139709] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Heavy metal contaminates have become a significant threat to soil ecosystems due to their chronicity and universality in soil. Soil microbial metabolism plays a vital role in biogeochemical cycles and soil functions. However, the response of microbial metabolism to heavy metal contamination in soil remains elusive despite potentially offering important insight into the health and ecological consequences of soil ecosystems under such contamination. This study used extracellular enzyme stoichiometry models to identify the response of microbial metabolism to various heavy metal contaminants, while also revealing potential implications of heavy metal contaminates in soil ecosystems. Results showed that microbial metabolism was restricted by soil carbon (C) and phosphorus (P) within a heavy metal polluted area in Northwest China. Heavy metal stress significantly increased microbial C limitation while decreasing microbial P limitation. However, microbial C and P limitations both responded consistently to different heavy metals (i.e., Cd, Pb, Zn, and Cu). Heavy metals had the greatest effect on microbial C limitation (i.e., 0.720 of the total effects) compared to other soil properties, and soil with the lowest heavy metal concentration exhibited the lowest microbial C limitation, and vice versa. These results indicated that microbial metabolic limitation can robustly and sensitively reflect the degree of heavy metals pollution in soil. Additionally, increased microbial C limitation caused by heavy metal contaminants could potentially escalate C release by promoting soil C decomposition as well as increasing investments in enzyme production and the maintenance of metabolic processes. Consequently, potential C loss induced by heavy metal pollution on soil ecosystems may be extensive and significant. Generally, our results suggest the usefulness of extracellular enzyme stoichiometry as a new method from which to evaluate heavy metal soil pollution, while microbial metabolic limitation could potentially be a promising indicator.
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Affiliation(s)
- Xia Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongxing Cui
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingchang Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China
| | - Wenliang Ju
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengjiao Duan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunqiang Wang
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China; State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment CAS, Xi'an 710061, China; Department of Earth and Environmental Sciences, Xi'an Jiaotong University, Xi'an 710049, China
| | - Linchuan Fang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation CAS and MWR, Yangling 712100, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
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Liu J, Yu X, Qin Q, Dinkins RD, Zhu H. The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes. Front Genet 2020; 11:00973. [PMID: 33014021 PMCID: PMC7461779 DOI: 10.3389/fgene.2020.00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/12/2023] Open
Abstract
Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.
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Affiliation(s)
- Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qiulin Qin
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Randy D Dinkins
- Forage-Animal Production Research Unit, United States Department of Agriculture-Agricultural Research Service, Lexington, KY, United States
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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Identification of tomato circular RNAs responsive to Phytophthora infestans. Gene 2020; 746:144652. [PMID: 32259631 DOI: 10.1016/j.gene.2020.144652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/27/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Circular RNAs (circRNAs), a novel branch of noncoding RNAs, are widespread in eukaryotic cells. Particularly, due to their abilities to bind microRNA (miRNA) and serve as "sponges", circRNAs can regulate gene expression and participate in multiple biological processes. To detect the function of the circRNAs in tomato resistance, in our study, high-throughput sequencing were used to detect the circRNAs in tomatoes before and after Phytophthora infestans (P. infestans) infection. A total of 68 circRNAs were identified, of them, 18 (26%) were termed as exonic circRNAs, 33 (49%) were termed as intergenic circRNAs, 17 (25%) were termed as intronic circRNAs. Thirty-six out of 68 circRNAs differentially expressed in tomatoes after infection, including 9 up- and 27 down-regulated. Among the up-regulated circRNAs, two exoinc circRNAs, circRNA45 and circRNA47 were annotated as whitefly-induced gp91-phox and ethylene-forming enzyme, respectively. Both of them could act as miR477-3p sponge. Transgenic plants transiently overexpressed circRNA45 and circRNA47 both displayed smaller lesion area than the control plants upon infection, accompanied by lower expression levels of miR477-3p. Furthermore, transiently overexpression of miR477-3p in tomatoes leading to a decline in their targeted disease related genes expression. Our results firstly identified circRNAs in tomato upon P. infestans infection and demonstrated that circRNA45 and circRNA47 may act as positive regulators in tomato resistance by regulating miRNA-mRNAs expression levels.
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Dussault‐Benoit C, Arsenault‐Labrecque G, Sonah H, Belzile F, Bélanger RR. Discriminant haplotypes of avirulence genes of Phytophthora sojae lead to a molecular assay to predict phenotypes. MOLECULAR PLANT PATHOLOGY 2020; 21:318-329. [PMID: 31908142 PMCID: PMC7036360 DOI: 10.1111/mpp.12898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 06/10/2023]
Abstract
The soybean-Phytophthora sojae interaction operates on a gene-for-gene relationship, where the product of a resistance gene (Rps) in the host recognizes that of an avirulence gene (Avr) in the pathogen to generate an incompatible reaction. To exploit this form of resistance, one must match with precision the appropriate Rps gene with the corresponding Avr gene. Currently, this association is evaluated by phenotyping assays that are labour-intensive and often imprecise. To circumvent this limitation, we sought to develop a molecular assay that would reveal the avirulence allele of the seven main Avr genes (Avr1a, Avr1b, Avr1c, Avr1d, Avr1k, Avr3a, and Avr6) in order to diagnose with precision the pathotypes of P. sojae isolates. For this purpose, we analysed the genomic regions of these Avr genes in 31 recently sequenced isolates with different virulence profiles and identified discriminant mutations between avirulence and virulence alleles. Specific primers were designed to generate amplicons of a distinct size, and polymerase chain reaction conditions were optimized in a final assay of two parallel runs. When tested on the 31 isolates of known virulence, the assay accurately revealed all avirulence alleles. The test was further assessed and compared to a phenotyping assay on 25 isolates of unknown virulence. The two assays matched in 97% (170/175) of the interactions studied. Interestingly, the sole cases of discrepancy were obtained with Avr3a, which suggests a possible imperfect interaction with Rps3a. This molecular assay offers a powerful and reliable tool to exploit and study with greater precision soybean resistance against P. sojae.
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Affiliation(s)
| | | | - Humira Sonah
- Department of PhytologyUniversité LavalQuébecQCCanada
- National Agri‐Food Biotechnology Institute (NABI)MohaliIndia
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50
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Fu X, Yang Y. WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0184-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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