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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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2
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Bamba M, Akyol TY, Azuma Y, Quilbe J, Andersen SU, Sato S. Synergistic effects of plant genotype and soil microbiome on growth in Lotus japonicus. FEMS Microbiol Ecol 2024; 100:fiae056. [PMID: 38678008 PMCID: PMC11068475 DOI: 10.1093/femsec/fiae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024] Open
Abstract
The biological interactions between plants and their root microbiomes are essential for plant growth, and even though plant genotype (G), soil microbiome (M), and growth conditions (environment; E) are the core factors shaping root microbiome, their relationships remain unclear. In this study, we investigated the effects of G, M, and E and their interactions on the Lotus root microbiome and plant growth using an in vitro cross-inoculation approach, which reconstructed the interactions between nine Lotus accessions and four soil microbiomes under two different environmental conditions. Results suggested that a large proportion of the root microbiome composition is determined by M and E, while G-related (G, G × M, and G × E) effects were significant but small. In contrast, the interaction between G and M had a more pronounced effect on plant shoot growth than M alone. Our findings also indicated that most microbiome variations controlled by M have little effect on plant phenotypes, whereas G × M interactions have more significant effects. Plant genotype-dependent interactions with soil microbes warrant more attention to optimize crop yield and resilience.
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Affiliation(s)
- Masaru Bamba
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Turgut Yigit Akyol
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Yusuke Azuma
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
| | - Johan Quilbe
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Stig Uggerhøj Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba, Sendai 980-8577, Japan
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Christian N, Perlin MH. Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes. Mycologia 2024; 116:227-250. [PMID: 38380970 DOI: 10.1080/00275514.2023.2299658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/22/2023] [Indexed: 02/22/2024]
Abstract
Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
| | - Michael H Perlin
- Department of Biology, University of Louisville, Louisville, Kentucky 40292
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Li Y, Tao S, Liang Y. Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae. J Fungi (Basel) 2024; 10:128. [PMID: 38392801 PMCID: PMC10890309 DOI: 10.3390/jof10020128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.
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Affiliation(s)
- Yunfan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, China
| | - Yingmei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
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Kovalev MA, Gladysh NS, Bogdanova AS, Bolsheva NL, Popchenko MI, Kudryavtseva AV. Editing Metabolism, Sex, and Microbiome: How Can We Help Poplar Resist Pathogens? Int J Mol Sci 2024; 25:1308. [PMID: 38279306 PMCID: PMC10816636 DOI: 10.3390/ijms25021308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Poplar (Populus) is a genus of woody plants of great economic value. Due to the growing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens. Genetic engineering can create organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly effective tool for creating valuable genotypes. In this review, we summarize the latest research data on poplar diseases, the biology of their pathogens and how these plants resist pathogens. In the final section, we propose to plant male or mixed poplar populations; consider the genes of the MLO group, transcription factors of the WRKY and MYB families and defensive proteins BbChit1, LJAMP2, MsrA2 and PtDef as the most promising targets for genetic engineering; and also pay attention to the possibility of microbiome engineering.
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Affiliation(s)
- Maxim A. Kovalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Natalya S. Gladysh
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Alina S. Bogdanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Institute of Agrobiotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, 127434 Moscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Mikhail I. Popchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia; (M.A.K.); (N.S.G.); (A.S.B.); (N.L.B.); (M.I.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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He C, Zhang M, Li X, He X. Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment. Front Plant Sci 2024; 14:1328586. [PMID: 38239215 PMCID: PMC10794659 DOI: 10.3389/fpls.2023.1328586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024]
Abstract
Introduction The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions. Methods In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica). Results The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants. Discussion This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.
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Affiliation(s)
- Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Man Zhang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding, China
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Van Nuland ME, Daws SC, Bailey JK, Schweitzer JA, Busby PE, Peay KG. Above- and belowground fungal biodiversity of Populus trees on a continental scale. Nat Microbiol 2023; 8:2406-2419. [PMID: 37973868 DOI: 10.1038/s41564-023-01514-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 10/04/2023] [Indexed: 11/19/2023]
Abstract
Understanding drivers of terrestrial fungal communities over large scales is an important challenge for predicting the fate of ecosystems under climate change and providing critical ecological context for bioengineering plant-microbe interactions in model systems. We conducted an extensive molecular and microscopy field study across the contiguous United States measuring natural variation in the Populus fungal microbiome among tree species, plant niche compartments and key symbionts. Our results show clear biodiversity hotspots and regional endemism of Populus-associated fungal communities explained by a combination of climate, soil and geographic factors. Modelling climate change impacts showed a deterioration of Populus mycorrhizal associations and an increase in potentially pathogenic foliar endophyte diversity and prevalence. Geographic differences among these symbiont groups in their sensitivity to environmental change are likely to influence broader forest health and ecosystem function. This dataset provides an above- and belowground atlas of Populus fungal biodiversity at a continental scale.
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Affiliation(s)
- Michael E Van Nuland
- Department of Biology, Stanford University, Stanford, CA, USA.
- Society for the Protection of Underground Networks, SPUN, Dover, DE, USA.
| | - S Caroline Daws
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joseph K Bailey
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Jennifer A Schweitzer
- Ecology and Evolutionary Biology Department, University of Tennessee, Knoxville, TN, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Earth System Science, Stanford University, Stanford, CA, USA
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023; 24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.
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Affiliation(s)
- Fantin Mesny
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Stéphane Hacquard
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Bart PHJ Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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Tie Z, Wang P, Chen W, Tang B, Yu Y, Liu Z, Zhao S, Khan FH, Zhang X, Xi H. Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars. Front Microbiol 2023; 14:1229454. [PMID: 37637103 PMCID: PMC10450913 DOI: 10.3389/fmicb.2023.1229454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.
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Affiliation(s)
- Zhanjiang Tie
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Peng Wang
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Weijian Chen
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Binghui Tang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, Xinjiang, China
| | - Yu Yu
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Zheng Liu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Sifeng Zhao
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Faisal Hayat Khan
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - XueKun Zhang
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Hui Xi
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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Belair M, Pensec F, Jany JL, Le Floch G, Picot A. Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding. Plants (Basel) 2023; 12:2383. [PMID: 37376008 DOI: 10.3390/plants12122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.
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Affiliation(s)
- Marie Belair
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Flora Pensec
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Jean-Luc Jany
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France
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12
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Li H, Tan L, Zhang C, Wei X, Wang Q, Li Q, Zheng X, Xu Y. Spatial distribution of bacterial resistance towards antibiotics of rural sanitation system in China and its potential link with diseases incidence. J Environ Sci (China) 2023; 127:361-374. [PMID: 36522068 DOI: 10.1016/j.jes.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 06/17/2023]
Abstract
Chinese government is vigorously promoting toilet renovation in rural areas to reduce the risk of human feces exposure, which would cause infectious diseases, especially antibiotic resistance genes (ARGs) and pathogens. However, the distribution of ARGs in human feces from different regions of China remained ill-defined. It is not yet known how the survival of ARGs after toilet treatment is associated with the regional infection rates. Here, we investigated the prevalence of ARGs in human feces in rural areas of China and their potential relationship with infectious diseases for the first large-scale. The results showed that there were still high ARGs residues in human feces after rural toilet treatment, especially tetM-01 and ermB with average relative abundance as high as 1.21 × 10-1 (Eastern) and 1.56 × 10-1 (Northern), respectively. At a large regional scale, the significant differences in human feces resistomes were mainly shaped by the toilet types, TN, NH3-N, and the bacterial community. A critical finding was that toilets still cannot effectively decrease the pathogenicity risk in human feces. The significant positive relationship (P<0.05) between infectious diseases and ARGs can infer that ARGs in human feces exposure might be a critical path for enhancing the incidence of diseases, as these ARGs hinder the effectiveness of antibiotics.
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Affiliation(s)
- Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Lu Tan
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Chunxue Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiaocheng Wei
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Qiang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Qian Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Xiangqun Zheng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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Zhang Y, Cao B, Pan Y, Tao S, Zhang N. Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species. Microbiol Spectr 2023; 11:e0383122. [PMID: 36916990 PMCID: PMC10101083 DOI: 10.1128/spectrum.03831-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.
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Affiliation(s)
- Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yumei Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
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14
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Sun M, Shi C, Huang Y, Wang H, Li J, Cai L, Luo F, Xiang L, Wang F. Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco. Front Microbiol 2023; 13:1081576. [PMID: 36687583 PMCID: PMC9846082 DOI: 10.3389/fmicb.2022.1081576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/09/2022] [Indexed: 01/05/2023] Open
Abstract
Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.
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Affiliation(s)
- Meili Sun
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, China,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Caihua Shi
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, China,School of Food Science and Technology & School of Chemical Engineering, Hubei University of Arts and Science, Xiangyang, Hubei, China,*Correspondence: Caihua Shi,
| | - Yang Huang
- China Tobacco Sichuan Industrial Corporation Technical Centre, Chengdu, China
| | - Hancheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China,Hancheng Wang,
| | - Jianjun Li
- College of Tropical Crops, Hainan University, Haikou Hainan, China
| | - Liuti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Fei Luo
- College of Life Science, Yangtze University, Jingzhou, China
| | - Ligang Xiang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China,Feng Wang,
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Chen KH, Marcón F, Duringer J, Blount A, Mackowiak C, Liao HL. Leaf Mycobiome and Mycotoxin Profile of Warm-Season Grasses Structured by Plant Species, Geography, and Apparent Black-Stroma Fungal Structure. Appl Environ Microbiol 2022;:e0094222. [PMID: 36226941 DOI: 10.1128/aem.00942-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Grasses harbor diverse fungi, including some that produce mycotoxins or other secondary metabolites. Recently, Florida cattle farmers reported cattle illness, while the cattle were grazing on warm-season grass pastures, that was not attributable to common causes, such as nutritional imbalances or nitrate toxicity. To understand correlations between grass mycobiome and mycotoxin production, we investigated the mycobiomes associated with five prominent, perennial forage and weed grasses [Paspalum notatum Flügge, Cynodon dactylon (L.) Pers., Paspalum nicorae Parodi, Sporobolus indicus (L.) R. Br., and Andropogon virginicus (L.)] collected from six Florida pastures actively grazed by livestock. Black fungal stromata of Myriogenospora and Balansia were observed on P. notatum and S. indicus leaves and were investigated. High-throughput amplicon sequencing was applied to delineate leaf mycobiomes. Mycotoxins from P. notatum leaves were inspected using liquid chromatography-mass spectrometry (LC-MS/MS). Grass species, cultivars, and geographic localities interactively affected fungal community assemblies of asymptomatic leaves. Among the grass species, the greatest fungal richness was detected in the weed S. indicus. The black fungal structures of P. notatum leaves were dominated by the genus Myriogenospora, while those of S. indicus were codominated by the genus Balansia and a hypermycoparasitic fungus of the genus Clonostachys. When comparing mycotoxins detected in P. notatum leaves with and without M. atramentosa, emodin, an anthraquinone, was the only compound which was significantly different (P < 0.05). Understanding the leaf mycobiome and the mycotoxins it may produce in warm-season grasses has important implications for how these associations lead to secondary metabolite production and their subsequent impact on animal health. IMPORTANCE The leaf mycobiome of forage grasses can have a major impact on their mycotoxin contents of forage and subsequently affect livestock health. Despite the importance of the cattle industry in warm-climate regions, such as Florida, studies have been primarily limited to temperate forage systems. Our study provides a holistic view of leaf fungi considering epibiotic, endophytic, and hypermycoparasitic associations with five perennial, warm-season forage and weed grasses. We highlight that plant identity and geographic location interactively affect leaf fungal community composition. Yeasts appeared to be an overlooked fungal group in healthy forage mycobiomes. Furthermore, we detected high emodin quantities in the leaves of a widely planted forage species (P. notatum) whenever epibiotic fungi occurred. Our study demonstrated the importance of identifying fungal communities, ecological roles, and secondary metabolites in perennial, warm-season grasses and their potential for interfering with livestock health.
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Shaker KH, Zohair MM, Hassan AZ, Sweelam HM, Ashour WE. LC-MS/MS and GC-MS based phytochemical perspectives and antimicrobial effects of endophytic fungus Chaetomium ovatoascomatis isolated from Euphorbia milii. Arch Microbiol 2022; 204:661. [PMID: 36192448 DOI: 10.1007/s00203-022-03262-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/21/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022]
Abstract
The antimicrobial activity of endophytic fungi isolated from Euphorbia milii was evaluated against Gram-positive, Gram-negative bacteria, unicellular yeast, and filamentous fungi. Chaetomium ovatoascomatis NRC was identified morphologically and genetically as the most active strain. The total ethyl acetate extract of C. ovatoascomatis NRC demonstrated significant antimicrobial activity against Gram-negative; Escherichia coli, Salmonella enteric, and fungi; Aspergillus niger with MIC of 62.5 ug/ml. Whereas n-hexane fraction demonstrated broader activity against Gram-positive; Bacillus subtilis, Lactobacillus cereus, Gram-negative; Escherichia coli and Salmonella enteric, fungi; Candida albicans and F. solani. LC–MS/MS analysis of ethyl acetate strain extract and GC–MS analysis of the n-hexane fraction were used to identify the metabolites of the strain extract. LC–MS/MS determined three major metabolites with potential antimicrobial activities including grevilline B, aflatoxin G2 and apigenin. GC–MS analysis of n-hexane fraction tentatively identified 30 compounds, where 9,12-octadecadienoic acid methyl ester was the major compound.
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17
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Dale JCM, Newman JA. A First Draft of the Core Fungal Microbiome of Schedonorus arundinaceus with and without Its Fungal Mutualist Epichloë coenophiala. J Fungi (Basel) 2022; 8:jof8101026. [PMID: 36294590 PMCID: PMC9605371 DOI: 10.3390/jof8101026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 11/26/2022] Open
Abstract
Tall fescue (Schedonorus arundinaceus) is a cool-season grass which is commonly infected with the fungal endophyte Epichloë coenophiala. Although the relationship between tall fescue and E. coenophiala is well-studied, less is known about its broader fungal communities. We used next-generation sequencing of the ITS2 region to describe the complete foliar fungal microbiomes in a set of field-grown tall fescue plants over two years, and whether these fungal communities were affected by the presence of Epichloë. We used the Georgia 5 cultivar of tall fescue, grown in the field for six years prior to sampling. Plants were either uninfected with E. coenophiala, or they were infected with one of two E. coenophiala strains: The common toxic strain or the AR542 strain (sold commerically as MaxQ). We observed 3487 amplicon sequence variants (ASVs) across all plants and identified 43 ASVs which may make up a potential core microbiome. Fungal communities did not differ strongly between Epichloë treatments, but did show a great deal of variation between the two years. Plant fitness also changed over time but was not influenced by E. coenophiala infection.
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Affiliation(s)
- Jenna C. M. Dale
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
| | - Jonathan A. Newman
- Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
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18
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Abstract
Tree planting and natural regeneration contribute to the ongoing effort to restore Earth's forests. Our review addresses how the plant microbiome can enhance the survival of planted and naturally regenerating seedlings and serve in long-term forest carbon capture and the conservation of biodiversity. We focus on fungal leaf endophytes, ubiquitous defensive symbionts that protect against pathogens. We first show that fungal and oomycetous pathogen richness varies greatly for tree species native to the United States (n = 0-876 known pathogens per US tree species), with nearly half of tree species either without pathogens in these major groups or with unknown pathogens. Endophytes are insurance against the poorly known and changing threat of tree pathogens. Next, we review studies of plant phyllosphere feedback, but knowledge gaps prevent us from evaluating whether adding conspecific leaf litter to planted seedlings promotes defensive symbiosis, analogous to adding soil to promote positive feedback. Finally, we discuss research priorities for integrating the plant microbiome into efforts to expand Earth's forests.
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Affiliation(s)
- Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, Idaho, USA
| | - Abigail S Neat
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA;
| | - Colin Averill
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
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19
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Dove NC, Carrell AA, Engle NL, Klingeman DM, Rodriguez M, Wahl T, Tschaplinski TJ, Muchero W, Schadt CW, Cregger MA. Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome. mSystems 2022;:e0012022. [PMID: 35862808 DOI: 10.1128/msystems.00120-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.
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Bao L, Sun B, Liu J, Zhang S, Xu N, Zhang X, Bohu T, Bai Z. Leaf-Associated Epiphytic Fungi of Gingko biloba, Pinus bungeana and Sabina chinensis Exhibit Delicate Seasonal Variations. J Fungi (Basel) 2022; 8:631. [PMID: 35736114 DOI: 10.3390/jof8060631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
Plant-leaf surface on Earth harbors complex microbial communities that influence plant productivity and health. To gain a detailed understanding of the assembly and key drivers of leaf microbial communities, especially for leaf-associated fungi, we investigated leaf-associated fungal communities in two seasons for three plant species at two sites by high-throughput sequencing. The results reveal a strong impact of growing season and plant species on fungal community composition, exhibiting clear temporal patterns in abundance and diversity. For the deciduous tree Gingko biloba, the number of enriched genera in May was much higher than that in October. The number of enriched genera in the two evergreen trees Pinus bungeana and Sabina chinensis was slightly higher in October than in May. Among the genus-level biomarkers, the abundances of Alternaria, Cladosporium and Filobasidium were significantly higher in October than in May in the three tree species. Additionally, network correlations between the leaf-associated fungi of G. biloba were more complex in May than those in October, containing extra negative associations, which was more obvious than the network correlation changes of leaf-associated fungi of the two evergreen plant species. Overall, the fungal diversity and community composition varied significantly between different growing seasons and host plant species.
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21
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Gervers KA, Thomas DC, Roy BA, Spatafora JW, Busby PE. Crown closure affects endophytic leaf mycobiome compositional dynamics over time in Pseudotsuga menziesii var. menziesii. FUNGAL ECOL 2022; 57-58:101155. [DOI: 10.1016/j.funeco.2022.101155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Tao S, Zhang Y, Tian C, Duplessis S, Zhang N. Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community. J Fungi (Basel) 2022; 8:jof8050523. [PMID: 35628778 PMCID: PMC9148057 DOI: 10.3390/jof8050523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O3 and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O3 and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O3 and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O3 or N addition only; however, the negative impact of elevated O3 could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O3 and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O3 and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O3, as determined by the markedly different abundance of taxa. Elevated O3 and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
| | | | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China; (S.T.); (Y.Z.); (C.T.)
- Correspondence:
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Shalev O, Ashkenazy H, Neumann M, Weigel D. Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms. ISME J 2022; 16:1235-1244. [PMID: 34897280 PMCID: PMC9038753 DOI: 10.1038/s41396-021-01168-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
AbstractPlants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.
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24
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Witzell J, Decker VHG, Agostinelli M, Romeralo C, Cleary M, Albrectsen BR. Aspen Leaves as a "Chemical Landscape" for Fungal Endophyte Diversity-Effects of Nitrogen Addition. Front Microbiol 2022; 13:846208. [PMID: 35387081 PMCID: PMC8978019 DOI: 10.3389/fmicb.2022.846208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.
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Affiliation(s)
- Johanna Witzell
- Forestry and Wood Technology, Linnaeus University, Växjö, Sweden.,Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Vicki Huizu Guo Decker
- Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Marta Agostinelli
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Carmen Romeralo
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Forest Research Centre (INIA, CSIC), Madrid, Spain
| | - Michelle Cleary
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Barge EG, Leopold DR, Rojas A, Vilgalys R, Busby PE. Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism. Mol Ecol 2022; 31:3018-3030. [DOI: 10.1111/mec.16436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Edward G. Barge
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Devin R. Leopold
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology University of Arkansas Fayetteville AR 72701 USA
| | - Rytas Vilgalys
- Department of Biology Duke University Durham NC 27708 USA
| | - Posy E. Busby
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
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26
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Hu H, Liu Y, Huang Y, Zhang Z, Tang H. The Leaf Microbiome of Tobacco Plants across Eight Chinese Provinces. Microorganisms 2022; 10:450. [PMID: 35208904 PMCID: PMC8878116 DOI: 10.3390/microorganisms10020450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 02/05/2023] Open
Abstract
Leaf microorganism communities play significant roles in the process of plant growth, but the microbiome profiling of crop leaves is still a relatively new research area. Here, we used 16S rDNA sequencing to profile the microbiomes of 78 primary dried tobacco leaf samples from 26 locations in eight Chinese provinces. Our analyses revealed that the national leaf microbial communities contain 4473 operational taxonomic units (OTU) representing 1234 species, but there is a small, national core microbiome with only 14 OTU representing nine species. The function of this core microbiome is related to processes including nitrogen fixation, detoxification of diverse pollutants, and heavy-metal reduction. The leaf microorganism communities are obviously affected by local environments but did not exhibit obvious relationships to single ecological factors (e.g., temperature, precipitation). Our findings enhance the understanding of microbial diversity of tobacco leaves, which could be utilized for a variety of bioprocess, agricultural, and environmental detoxification applications.
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27
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Grabka R, d’Entremont TW, Adams SJ, Walker AK, Tanney JB, Abbasi PA, Ali S. Fungal Endophytes and Their Role in Agricultural Plant Protection against Pests and Pathogens. Plants (Basel) 2022; 11:plants11030384. [PMID: 35161365 PMCID: PMC8840373 DOI: 10.3390/plants11030384] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 05/06/2023]
Abstract
Virtually all examined plant species harbour fungal endophytes which asymptomatically infect or colonize living plant tissues, including leaves, branches, stems and roots. Endophyte-host interactions are complex and span the mutualist-pathogen continuum. Notably, mutualist endophytes can confer increased fitness to their host plants compared with uncolonized plants, which has attracted interest in their potential application in integrated plant health management strategies. In this review, we report on the many benefits that fungal endophytes provide to agricultural plants against common non-insect pests such as fungi, bacteria, nematodes, viruses, and mites. We report endophytic modes of action against the aforementioned pests and describe why this broad group of fungi is vitally important to current and future agricultural practices. We also list an extensive number of plant-friendly endophytes and detail where they are most commonly found or applied in different studies. This review acts as a general resource for understanding endophytes as they relate to potential large-scale agricultural applications.
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Affiliation(s)
- Rachel Grabka
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Tyler W. d’Entremont
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Sarah J. Adams
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada; (T.W.d.); (S.J.A.); (A.K.W.)
| | - Joey B. Tanney
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 Burnside Road West, Victoria, BC V8Z 1M5, Canada;
| | - Pervaiz A. Abbasi
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
| | - Shawkat Ali
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS B4N 1J5, Canada; (R.G.); (P.A.A.)
- Correspondence:
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28
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Liu L, Yang C, Xu X, Wang X, Liu M, Chen R, Tan F, Liu Y, Lin T, Liu Y. Unlocking the Changes of Phyllosphere Fungal Communities of Fishscale Bamboo (Phyllachora heterocladae) under Rhombic-Spot Disease Stressed Conditions. Forests 2022; 13:185. [DOI: 10.3390/f13020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As an important nonwood bioresource, fishscale bamboo (Phyllachora heterocladae Oliver) is widely distributed in the subtropical region of China. Rhombic-spot disease, caused by Neostagonosporella sichuanensis, is one of the most serious diseases that threatens fishscale bamboo health. However, there is limited knowledge about how rhombic-spot disease influences the diversity and structures of phyllosphere fungal communities. In this study, we investigated the phyllosphere fungal communities from stems, branches, and leaves of fishscale bamboo during a rhombic-spot disease outbreak using 18S rRNA sequencing. We found that only the phyllosphere fungal community from stems was significantly affected by pathogen invasion in terms of community richness, diversity, and structure. FUNGuild analysis revealed that the major classifications of phyllosphere fungi based on trophic modes in stems, branches, and leaves changed from symbiotroph-pathotroph, no obvious dominant trophic mode, and symbiotroph to saprotroph, saprotroph–pathotroph–symbiotroph, and saprotroph–symbiotroph, respectively, after pathogen invasion. The fungal community composition of the three tissues displayed significant differences at the genus level between healthy and diseased plants. The associations among fungal species in diseased samples showed more complex co-occurrence network structures than those of healthy samples. Taken together, our results highlight the importance of plant pathological conditions for the assembly of phyllosphere fungal communities in different tissues.
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29
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May G, Shaw RG, Geyer CJ, Eck DJ. Do Interactions among Microbial Symbionts Cause Selection for Greater Pathogen Virulence? Am Nat 2022; 199:252-265. [DOI: 10.1086/717679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Ruth G. Shaw
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Charles J. Geyer
- School of Statistics, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel J. Eck
- Department of Statistics, University of Illinois, Champaign, Illinois 61820
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30
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Zahn G. Marker Genes (16S and ITS) Protocol for Plant Microbiome Analyses. Bio Protoc 2022. [DOI: 10.21769/bioprotoc.4395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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31
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Zhang Y, Long Z, Yan L, Liu L, Yang L, Le Y. Discovery of 4-nitro-3-phenylisoxazole derivatives as potent antibacterial agents derived from the studies of [3 + 2] cycloaddition. RSC Adv 2022; 12:25633-25638. [PMID: 36199305 PMCID: PMC9455768 DOI: 10.1039/d2ra05009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/21/2022] [Indexed: 12/04/2022] Open
Abstract
Polysubstituted phenylisoxazoles were designed and synthesized to discover new antibacterial agents via [3 + 2] cycloaddition. Thirty-five compounds with a phenylisoxazole scaffold were characterized by NMR, HRMS, and X-ray techniques. After being evaluated against Xanthomonas oryzae (Xoo), Pseudomonas syringae (Psa), and Xanthomonas axonopodis (Xac), 4-nitro-3-phenylisoxazole derivatives were found to better antibacterial activities. Further studies have shown that the EC50 values of these compounds were much better than that of the positive control, bismerthiazol. Thirty-five compounds with phenylisoxazole scaffold were synthesized via [3+2] cycloaddition. After being evaluated against Xoo, Psa and Xac, 4-nitro-3-phenylisoxazole derivatives were found well antibacterial activities.![]()
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Affiliation(s)
- Yan Zhang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Zhiwu Long
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Longjia Yan
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guiyang 550025, China
| | - Li Liu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guiyang 550025, China
| | - Lan Yang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guiyang 550025, China
| | - Yi Le
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guiyang 550025, China
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32
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Abstract
The microorganisms associated with an organism, the microbiome, have a strong and wide impact in their host biology. In particular, the microbiome modulates both the host defense responses and immunity, thus influencing the fate of infections by pathogens. Indeed, this immune modulation and/or interaction with pathogenic viruses can be essential to define the outcome of viral infections. Understanding the interplay between the microbiome and pathogenic viruses opens future venues to fight viral infections and enhance the efficacy of antiviral therapies. An increasing number of researchers are focusing on microbiome-virus interactions, studying diverse combinations of microbial communities, hosts, and pathogenic viruses. Here, we aim to review these studies, providing an integrative overview of the microbiome impact on viral infection across different pathosystems.
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33
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Wille L, Kurmann M, Messmer MM, Studer B, Hohmann P. Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health. Front Plant Sci 2021; 12:737820. [PMID: 34712258 PMCID: PMC8545811 DOI: 10.3389/fpls.2021.737820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Mario Kurmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Monika M. Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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34
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Zaret MM, Bauer JT, Clay K, Whitaker BK. Conspecific leaf litter induces negative feedbacks in Asteraceae seedlings. Ecology 2021; 102:e03557. [PMID: 34625950 DOI: 10.1002/ecy.3557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/07/2021] [Accepted: 07/23/2021] [Indexed: 11/07/2022]
Abstract
The plant soil feedback (PSF) framework has been instrumental in understanding the impacts of soil microbes on plant fitness and species coexistence. PSFs develop when soil microbial communities are altered due to the identity and density of a particular plant species, which can then enhance or inhibit the local survival and growth of that plant species as well as different plant species. The recent extension of the PSF framework to aboveground microbiota, termed here as plant phyllosphere feedbacks (PPFs), can also help to determine the impact of aboveground microbes on plant fitness and species interactions. However, experimental tests of PPFs during early plant growth are nascent and the prevalence of PPFs across diverse plant species remains unknown. Additionally, it is unclear whether plant host characteristics, such as functional traits or phylogenetic distance, may help to predict the strength and direction of PPFs. To test for the prevalence of litter-mediated PPFs, recently senesced plant litter from 10 native Asteraceae species spanning a range of life history strategies was used to inoculate seedlings of both conspecific and heterospecific species. We found that exposure to conspecific litter significantly reduced the growth of four species relative to exposure to heterospecific litter (i.e., significant negative PPFs), three species experienced marginally significant negative PPFs, and the PPF estimates for all 10 species were negative. However, neither plant functional traits, nor phylogenetic distance were predictive of litter feedbacks across plant species pairs, suggesting that other mechanisms or traits not measured may be driving conspecific negative PPFs. Our results indicate that negative, litter-mediated PPFs are common among native Asteraceae species and that they may have substantial impacts on plant growth and plant species interactions, particularly during early plant growth.
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Affiliation(s)
- Max M Zaret
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jonathan T Bauer
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Biology, Miami University, Oxford, Ohio, USA.,Institute for the Environment and Sustainability, Miami University, Oxford, Ohio, USA
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Briana K Whitaker
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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35
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Olivieri L, Saville RJ, Gange AC, Xu X. Apple endophyte community in relation to location, scion and rootstock genotypes and susceptibility to European canker. FEMS Microbiol Ecol 2021; 97:fiab131. [PMID: 34601593 PMCID: PMC8497447 DOI: 10.1093/femsec/fiab131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
European apple canker, caused by Neonectria ditissima, is a severe disease of apple. Achieving effective control is difficult with the currently available pesticides. Specific apple endophytes associated with cultivars may partially contribute to the cultivar response to the pathogen and thus could be used for disease management. We sought to determine whether the overall endophyte community differed among cultivars differing in their susceptibility to N. ditissima and to identify specific microbial groups associated with the susceptibility. Using Illumina MiSeq meta-barcoding, we profiled apple tree endophytes in 16 scion-rootstock combinations at two locations and quantified the relative contribution of scion, rootstock and location to the observed variability in the endophyte communities. Endophyte diversity was primarily affected by the orchard location (accounting for 29.4% and 85.9% of the total variation in the PC1 for bacteria and fungi, respectively), followed by the scion genotype (24.3% and 19.5% of PC2), whereas rootstock effects were small (<3% of PC1 and PC2). There were significant differences in the endophyte community between canker-resistant and -susceptible cultivars. Several bacterial and fungal endophyte groups had different relative abundance between susceptible and resistant cultivars. These endophyte groups included putative pathogen antagonists as well as plant pathogens. Their possible ecological roles in the N. ditissima pathosystem are discussed.
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Affiliation(s)
- Leone Olivieri
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Robert J Saville
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
- Agriculture & Horticulture Development Board, Stoneleigh Park, Kenilworth, Warwickshire CV8 2TL, UK
| | - Alan C Gange
- Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Xiangming Xu
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, UK
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36
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Harrison JG, Beltran LP, Buerkle CA, Cook D, Gardner DR, Parchman TL, Poulson SR, Forister ML. A suite of rare microbes interacts with a dominant, heritable, fungal endophyte to influence plant trait expression. ISME J 2021; 15:2763-2778. [PMID: 33790425 PMCID: PMC8397751 DOI: 10.1038/s41396-021-00964-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 02/08/2021] [Accepted: 03/15/2021] [Indexed: 01/31/2023]
Abstract
Endophytes are microbes that live, for at least a portion of their life history, within plant tissues. Endophyte assemblages are often composed of a few abundant taxa and many infrequently observed, low-biomass taxa that are, in a word, rare. The ways in which most endophytes affect host phenotype are unknown; however, certain dominant endophytes can influence plants in ecologically meaningful ways-including by affecting growth and immune system functioning. In contrast, the effects of rare endophytes on their hosts have been unexplored, including how rare endophytes might interact with abundant endophytes to shape plant phenotype. Here, we manipulate both the suite of rare foliar endophytes (including both fungi and bacteria) and Alternaria fulva-a vertically transmitted and usually abundant fungus-within the fabaceous forb Astragalus lentiginosus. We report that rare, low-biomass endophytes affected host size and foliar %N, but only when the heritable fungal endophyte (A. fulva) was not present. A. fulva also reduced plant size and %N, but these deleterious effects on the host could be offset by a negative association we observed between this heritable fungus and a foliar pathogen. These results demonstrate how interactions among endophytic taxa determine the net effects on host plants and suggest that the myriad rare endophytes within plant leaves may be more than a collection of uninfluential, commensal organisms, but instead have meaningful ecological roles.
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Affiliation(s)
- Joshua G. Harrison
- grid.135963.b0000 0001 2109 0381Department of Botany, University of Wyoming, Laramie, WY USA
| | - Lyra P. Beltran
- grid.266818.30000 0004 1936 914XEcology, Evolution, and Conservation Biology Program, Biology Department, University of Nevada, Reno, NV USA
| | - C. Alex Buerkle
- grid.135963.b0000 0001 2109 0381Department of Botany, University of Wyoming, Laramie, WY USA
| | - Daniel Cook
- grid.417548.b0000 0004 0478 6311Poisonous Plant Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Logan, UT USA
| | - Dale R. Gardner
- grid.417548.b0000 0004 0478 6311Poisonous Plant Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Logan, UT USA
| | - Thomas L. Parchman
- grid.266818.30000 0004 1936 914XEcology, Evolution, and Conservation Biology Program, Biology Department, University of Nevada, Reno, NV USA
| | - Simon R. Poulson
- grid.266818.30000 0004 1936 914XDepartment of Geological Sciences & Engineering, University of Nevada, Reno, NV USA
| | - Matthew L. Forister
- grid.266818.30000 0004 1936 914XEcology, Evolution, and Conservation Biology Program, Biology Department, University of Nevada, Reno, NV USA
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37
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Hawkes CV, Kjøller R, Raaijmakers JM, Riber L, Christensen S, Rasmussen S, Christensen JH, Dahl AB, Westergaard JC, Nielsen M, Brown-Guedira G, Hestbjerg Hansen L. Extension of Plant Phenotypes by the Foliar Microbiome. Annu Rev Plant Biol 2021; 72:823-846. [PMID: 34143648 DOI: 10.1146/annurev-arplant-080620-114342] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.
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Affiliation(s)
- Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Jesper Cairo Westergaard
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service and Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
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38
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Lekberg Y, Arnillas CA, Borer ET, Bullington LS, Fierer N, Kennedy PG, Leff JW, Luis AD, Seabloom EW, Henning JA. Nitrogen and phosphorus fertilization consistently favor pathogenic over mutualistic fungi in grassland soils. Nat Commun 2021; 12:3484. [PMID: 34108462 PMCID: PMC8190096 DOI: 10.1038/s41467-021-23605-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/03/2021] [Indexed: 02/05/2023] Open
Abstract
Ecosystems across the globe receive elevated inputs of nutrients, but the consequences of this for soil fungal guilds that mediate key ecosystem functions remain unclear. We find that nitrogen and phosphorus addition to 25 grasslands distributed across four continents promotes the relative abundance of fungal pathogens, suppresses mutualists, but does not affect saprotrophs. Structural equation models suggest that responses are often indirect and primarily mediated by nutrient-induced shifts in plant communities. Nutrient addition also reduces co-occurrences within and among fungal guilds, which could have important consequences for belowground interactions. Focusing only on plots that received no nutrient addition, soil properties influence pathogen abundance globally, whereas plant community characteristics influence mutualists, and climate influence saprotrophs. We show consistent, guild-level responses that enhance our ability to predict shifts in soil function related to anthropogenic eutrophication, which can have longer-term consequences for plant communities.
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Affiliation(s)
- Ylva Lekberg
- MPG Ranch, Missoula, MT USA ,grid.253613.00000 0001 2192 5772Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT USA
| | - Carlos A. Arnillas
- grid.17063.330000 0001 2157 2938Department of Physical and Environmental Sciences, University of Toronto – Scarborough, Scarborough, Canada
| | - Elizabeth T. Borer
- grid.17635.360000000419368657Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN USA
| | | | - Noah Fierer
- grid.266190.a0000000096214564Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO USA ,grid.464551.70000 0004 0450 3000Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO USA
| | - Peter G. Kennedy
- grid.17635.360000000419368657Departments of Plant Biology and Ecology, University of Minnesota, St Paul, MN USA
| | | | - Angela D. Luis
- grid.253613.00000 0001 2192 5772Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT USA
| | - Eric W. Seabloom
- grid.17635.360000000419368657Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN USA
| | - Jeremiah A. Henning
- grid.17635.360000000419368657Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN USA ,grid.267153.40000 0000 9552 1255Department of Biology, University of South Alabama, Mobile, AL USA
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Wenndt AJ, Evans SE, van Diepeningen AD, Logan JR, Jacobson PJ, Seely MK, Jacobson KM. Why Plants Harbor Complex Endophytic Fungal Communities: Insights From Perennial Bunchgrass Stipagrostis sabulicola in the Namib Sand Sea. Front Microbiol 2021; 12:691584. [PMID: 34168636 PMCID: PMC8217645 DOI: 10.3389/fmicb.2021.691584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/10/2021] [Indexed: 01/16/2023] Open
Abstract
All perennial plants harbor diverse endophytic fungal communities, but why they tolerate these complex asymptomatic symbioses is unknown. Using a multi-pronged approach, we conclusively found that a dryland grass supports endophyte communities comprised predominantly of latent saprophytes that can enhance localized nutrient recycling after senescence. A perennial bunchgrass, Stipagrostis sabulicola, which persists along a gradient of extreme abiotic stress in the hyper-arid Namib Sand Sea, was the focal point of our study. Living tillers yielded 20 fungal endophyte taxa, 80% of which decomposed host litter during a 28-day laboratory decomposition assay. During a 6-month field experiment, tillers with endophytes decomposed twice as fast as sterilized tillers, consistent with the laboratory assay. Furthermore, profiling the community active during decomposition using next-generation sequencing revealed that 59-70% of the S. sabulicola endophyte community is comprised of latent saprophytes, and these dual-niche fungi still constitute a large proportion (58-62%) of the litter community more than a year after senescence. This study provides multiple lines of evidence that the fungal communities that initiate decomposition of standing litter develop in living plants, thus providing a plausible explanation for why plants harbor complex endophyte communities. Using frequent overnight non-rainfall moisture events (fog, dew, high humidity), these latent saprophytes can initiate decomposition of standing litter immediately after tiller senescence, thus maximizing the likelihood that plant-bound nutrients are recycled in situ and contribute to the nutrient island effect that is prevalent in drylands.
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Affiliation(s)
- Anthony J Wenndt
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Sarah E Evans
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States.,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Anne D van Diepeningen
- B.U. Biointeractions and Plant Health, Wageningen Plant Research, Wageningen University and Research, Wageningen, Netherlands
| | - J Robert Logan
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States.,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
| | - Peter J Jacobson
- Department of Biology, Grinnell College, Grinnell, IA, United States
| | - Mary K Seely
- Desert Research Foundation of Namibia, Windhoek, Namibia
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Heitmann S, Bergmann GE, Barge E, Ridout M, Newcombe G, Busby PE. Culturable Seed Microbiota of Populus trichocarpa. Pathogens 2021; 10:653. [PMID: 34074042 DOI: 10.3390/pathogens10060653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/09/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022] Open
Abstract
Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, Populus trichocarpa, collected from different sites. We found that individual P. trichocarpa seeds typically contained zero or one microbe, with common taxa including species of Cladosporium, Aureobasidium, Diaporthe, Alternaria, and Pseudomonas, a bacterium. Pseudomonas isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within Epicoccum, Alternaria, and Aureobasidium from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, Pseudomonas syringae pv. syringae, and found that it reduced seed germination and increased seedling mortality for P. trichocarpa. Our findings highlight common fungi and bacteria in the seeds of P. trichocarpa, prompting further study of their functional consequences. Moreover, our study confirms that P. syringae pv. syringae is a seed pathogen of P. trichocarpa and is the first report that P. syringae pv. syringae is a lethal seedling pathogen of P. trichocarpa, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.
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41
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O'Keeffe KR, Halliday FW, Jones CD, Carbone I, Mitchell CE. Parasites, niche modification and the host microbiome: A field survey of multiple parasites. Mol Ecol 2021; 30:2404-2416. [PMID: 33740826 DOI: 10.1111/mec.15892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 01/04/2023]
Abstract
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.
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Affiliation(s)
- Kayleigh R O'Keeffe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fletcher W Halliday
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Charles E Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
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42
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43
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Liu X, Jia P, Cadotte MW, Zhu C, Si X, Wang Y, Chen F, Wu J, Zhou S. Host plant environmental filtering drives foliar fungal community assembly in symptomatic leaves. Oecologia 2021; 195:737-49. [PMID: 33582871 DOI: 10.1007/s00442-021-04849-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022]
Abstract
Foliar fungi (defined as all fungal species in leaves after surface sterilization; hereafter, 'FF') are of great importance to host plant growth and health, and can also affect ecosystem functioning. Despite this importance, few studies have explicitly examined the role of host filtering in shaping local FF communities, and we know little about the differences of FF community assembly between symptomatic (caused by fungal pathogens) and asymptomatic leaves, and whether there is phylogenetic congruence between host plants and FF. We examined FF communities from 25 host plant species (for each species, symptomatic and asymptomatic leaves, respectively) in an alpine meadow of the Tibetan Plateau using MiSeq sequencing of ITS1 gene biomarkers. We evaluated the phylogenetic congruence of FF-plant interactions based on cophylogenetic analysis, and examined α- and β-phylogenetic diversity indices of the FF communities. We found strong support for phylogenetic congruence between host plants and FF for both asymptomatic and symptomatic leaves, and a host-caused filter appears to play a major role in shaping FF communities. Most importantly, we provided independent lines of evidence that host environmental filtering (caused by fungal infections) outweighs competitive exclusion in driving FF community assembly in symptomatic leaves. Our results help strengthen the foundation of FF community assembly by demonstrating the importance of host environmental filtering in driving FF community assembly.
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Abstract
Plants host diverse microbial communities, but there is little consensus on how we sample these communities, and this has unknown consequences. Using root and leaf tissue from showy milkweed (Asclepias speciosa), we compared two common sampling strategies: (1) homogenizing after subsampling (30 mg), and (2) homogenizing bulk tissue before subsampling (30 mg). We targeted bacteria, arbuscular mycorrhizal (AM) fungi and non-AM fungi in roots, and foliar fungal endophytes (FFE) in leaves. We further extracted DNA from all of the leaf tissue collected to determine the extent of undersampling of FFE, and sampled FFE twice across the season using strategy one to assess temporal dynamics. All microbial groups except AM fungi differed in composition between the two sampling strategies. Community overlap increased when rare taxa were removed, but FFE and bacterial communities still differed between strategies, with largely non-overlapping communities within individual plants. Increasing the extraction mass 10 × increased FFE richness ~ 10 ×, confirming the severe undersampling indicated in the sampling comparisons. Still, seasonal patterns in FFEs were apparent, suggesting that strong drivers are identified despite severe undersampling. Our findings highlight that current sampling practices poorly characterize many microbial groups, and increased sampling intensity is necessary for increase reproducibility and to identify subtler patterns in microbial distributions.
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Affiliation(s)
- Lorinda S Bullington
- MPG Ranch, Missoula, MT, 59801, USA.
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA.
| | - Ylva Lekberg
- MPG Ranch, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
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Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. J Exp Bot 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
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Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
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Eitzen K, Sengupta P, Kroll S, Kemen E, Doehlemann G. A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme. eLife 2021; 10:65306. [PMID: 33427195 PMCID: PMC7870139 DOI: 10.7554/elife.65306] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 12/22/2022] Open
Abstract
Plants are not only challenged by pathogenic organisms but also colonized by commensal microbes. The network of interactions these microbes establish with their host and among each other is suggested to contribute to the immune responses of plants against pathogens. In wild Arabidopsis thaliana populations, the oomycete pathogen Albugo laibachii plays an influential role in structuring the leaf phyllosphere. We show that the epiphytic yeast Moesziomyces bullatus ex Albugo on Arabidopsis, a close relative of pathogenic smut fungi, is an antagonistic member of the A. thaliana phyllosphere, which reduces infection of A. thaliana by A. laibachii. Combination of transcriptomics, reverse genetics, and protein characterization identified a GH25 hydrolase with lysozyme activity as a major effector of this microbial antagonism. Our findings broaden the understanding of microbial interactions within the phyllosphere, provide insights into the evolution of epiphytic basidiomycete yeasts, and pave the way for novel biocontrol strategies.
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Affiliation(s)
- Katharina Eitzen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne, Germany
| | - Samuel Kroll
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Tübingen, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne, Germany
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Fang K, Chen L, Zhang H. Evaluation of foliar fungus-mediated interactions with below and aboveground enemies of the invasive plant Ageratina adenophora. Ecol Evol 2021; 11:526-535. [PMID: 33437448 PMCID: PMC7790651 DOI: 10.1002/ece3.7072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 11/09/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022] Open
Abstract
Plant-fungal associations are frequently key drivers of plant invasion success. Foliar fungi can benefit their invasive hosts by enhancing growth promotion, disease resistance and environmental stress tolerance. However, the roles of foliar fungi may vary when a given invasive plant faces different stresses. In this study, we designed three independent experiments to evaluate the effects of a foliar fungus, Colletotrichum sp., on the growth performance of the invasive plant Ageratina adenophora under different soil conditions, as well as the responses of A. adenophora to the foliar fungal pathogen Diaporthe helianthi and to herbivory. We found that the soil type was the most influential factor for the growth of A. adenophora. The role of the foliar fungus Colletotrichum sp. varied in the different soil types but generally adversely affected leaf development in A. adenophora. Colletotrichum sp. may be a weak latent foliar pathogen that can enhance the pathogenicity of D. helianthi on leaves of A. adenophora and marginally reduce signs of herbivory by natural insects in the wild on A. adenophora seedlings. In general, the benefits of the foliar fungus Colletotrichum to the fitness of A. adenophora are not significant in the context of this experimental design. However, our data highlight the need to consider both aboveground and belowground biota in different soil habitats when evaluating the effects of foliar fungi.
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Affiliation(s)
- Kai Fang
- School of Ecology and Environmental ScienceYunnan UniversityKunmingChina
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
| | - Li‐Min Chen
- Sichuan Academy of Grassland SciencesChengduChina
| | - Han‐Bo Zhang
- School of Ecology and Environmental ScienceYunnan UniversityKunmingChina
- State Key Laboratory for Conservation and Utilization of Bio‐Resources in YunnanYunnan UniversityKunmingChina
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48
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Newcombe G, Fraser SJ, Ridout M, Busby PE. Leaf Endophytes of Populus trichocarpa Act as Pathogens of Neighboring Plant Species. Front Microbiol 2020; 11:573056. [PMID: 33281769 PMCID: PMC7705171 DOI: 10.3389/fmicb.2020.573056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/15/2020] [Indexed: 11/22/2022] Open
Abstract
The conventional definition of endophytes is that they do not cause disease, whereas pathogens do. Complicating this convention, however, is the poorly explored phenomenon that some microbes are endophytes in some plants but pathogens in others. Black cottonwood or poplar (Populus trichocarpa) and wheat (Triticum aestivum) are common wild and crop plants, respectively, in the Pacific Northwest USA. The former anchors wild, riparian communities, whereas the latter is an introduced domesticate of commercial importance in the region. We isolated Fusarium culmorum – a well-known pathogen of wheat causing both blight and rot – from the leaf of a black cottonwood tree in western Washington. The pathogenicity of this cottonwood isolate and of a wheat isolate of F. culmorum were compared by inoculating both cottonwood and wheat in a greenhouse experiment. We found that both the cottonwood and wheat isolates of F. culmorum significantly reduced the growth of wheat, whereas they had no impact on cottonwood growth. Our results demonstrate that the cottonwood isolate of F. culmorum is endophytic in one plant species but pathogenic in another. Using sequence-based methods, we found an additional 56 taxa in the foliar microbiome of cottonwood that matched the sequences of pathogens of other plants of the region. These sequence-based findings suggest, though they do not prove, that P. trichocarpa may host many additional pathogens of other plants.
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Affiliation(s)
- George Newcombe
- Department of Forest, Rangeland, and Fire Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Shannon J Fraser
- Department of Forest, Rangeland, and Fire Sciences, College of Natural Resources, University of Idaho, Moscow, ID, United States
| | - Mary Ridout
- College of Agriculture and Life Sciences, University of Idaho Extension Washington County, Weiser, ID, United States
| | - Posy E Busby
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR, United States
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Abstract
The assembly of fungal endophyte communities within plants depends on the complex interactions of fungal taxa, their host plants, and the abiotic environment. Prairie plant communities provide a unique avenue to explore the interplay of biotic and abiotic factors affecting endophyte communities, since the historical distribution of prairies spans a broad range of temperature and precipitation, while the distances between small fragments of contemporary prairie communities may challenge the dispersal capabilities of these otherwise ubiquitous fungi. We sampled foliar fungal endophytes from two native prairie legumes, purple and white prairie clovers (Dalea purpurea and D. candida), in 17 remnant prairie sites across Minnesota in order to evaluate the relative contributions of abiotic factors, host species, and dispersal limitation to the diversity and structure of these communities. We found that similarity of communities was significantly associated with their location along a temperature and precipitation gradient, and we showed a distance-decay relationship that suggests dispersal limitations only over very large spatial scales. Although the effect of host species was small relative to these other factors, the two Dalea species maintained distinct communities within sites where they co-occur. Our results illustrate the capacity of many of these endophyte taxa to disperse over large distances and across heterogeneous biotic and abiotic environments and suggest that the interplay of biotic and abiotic factors maintains high diversity observed in endophyte communities.
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Affiliation(s)
- Mara DeMers
- Plant and Microbial Biology Graduate Program, University of Minnesota , St. Paul, Minnesota 55108
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota , St. Paul, Minnesota 55108
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50
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Wagner MR, Roberts JH, Balint-Kurti P, Holland JB. Heterosis of leaf and rhizosphere microbiomes in field-grown maize. New Phytol 2020; 228:1055-1069. [PMID: 32521050 DOI: 10.1111/nph.16730] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/28/2020] [Indexed: 05/21/2023]
Abstract
Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
| | - Joseph H Roberts
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
| | - James B Holland
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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