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Laurent‐Webb L, Maurice K, Perez‐Lamarque B, Bourceret A, Ducousso M, Selosse M. Seed or soil: Tracing back the plant mycobiota primary sources. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13301. [PMID: 38924368 PMCID: PMC11194045 DOI: 10.1111/1758-2229.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/13/2024] [Indexed: 06/28/2024]
Abstract
Plants host diverse communities of fungi (the mycobiota), playing crucial roles in their development. The assembly processes of the mycobiota, however, remain poorly understood, in particular, whether it is transmitted by parents through the seeds (vertical transmission) or recruited in the environment (horizontal transmission). Here we attempt to quantify the relative contributions of horizontal and vertical transmission in the mycobiota assembly of a desert shrub, Haloxylon salicornicum, by comparing the mycobiota of in situ bulk soil and seeds to that of (i) in situ adult individuals and (ii) in vitro-germinated seedlings in soil collected in situ. We show that the mycobiota are partially vertically transmitted through the seeds to seedlings, whereas bulk soil has a limited contribution to the seedling's mycobiota. In adults, root and bulk soil mycobiota tend to resemble each other, suggesting a compositional turnover in plant mycobiota during plant development due to horizontal transmission. Thus, the mycobiota are transmitted both horizontally and vertically depending on the plant tissue and developmental stage. Understanding the respective contribution of these transmission pathways to the plant mycobiota is fundamental to deciphering potential coevolutionary processes between plants and fungi. Our findings particularly emphasize the importance of vertical transmission in desert ecosystems.
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Affiliation(s)
- Liam Laurent‐Webb
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHEParisFrance
| | | | - Benoît Perez‐Lamarque
- Institut de Biologie de l'École Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Amélia Bourceret
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHEParisFrance
| | | | - Marc‐André Selosse
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRSSorbonne Université, EPHEParisFrance
- Faculty of BiologyUniversity of GdanskGdanskPoland
- Institut Universitaire de FranceParisFrance
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2
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Sierra AM, Meléndez O, Bethancourt R, Bethancourt A, Rodríguez-Castro L, López CA, Sedio BE, Saltonstall K, Villarreal A JC. Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms. J Chem Ecol 2024:10.1007/s10886-024-01511-z. [PMID: 38809282 DOI: 10.1007/s10886-024-01511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.
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Affiliation(s)
- Adriel M Sierra
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
| | - Omayra Meléndez
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Rita Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Ariadna Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Lilisbeth Rodríguez-Castro
- Departamento de Microbiología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Christian A López
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
- Smithsonian Tropical Research Institute, Ancón, Panamá.
- Canada Research Chair in Genomics of Tropical Symbioses, Department of Biology, Université Laval, Québec, G1V 0A6, Canadá.
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [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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O'Brien AM, Laurich JR, Frederickson ME. Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability. Evolution 2024; 78:237-252. [PMID: 37828761 DOI: 10.1093/evolut/qpad183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/30/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
An organism's phenotypes and fitness often depend on the interactive effects of its genome (Ghost), microbiome (Gmicrobe), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured Lemnaminor (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.minor fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.
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Affiliation(s)
- Anna M O'Brien
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason R Laurich
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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Schmidt JE, Puig AS, DuVal AE, Pfeufer EE. Phyllosphere microbial diversity and specific taxa mediate within-cultivar resistance to Phytophthora palmivora in cacao. mSphere 2023; 8:e0001323. [PMID: 37603690 PMCID: PMC10597403 DOI: 10.1128/msphere.00013-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/08/2023] [Indexed: 08/23/2023] Open
Abstract
The oomycete pathogen Phytophthora palmivora, which causes black pod rot (BPR) on cacao (Theobroma cacao L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to Phytophthora spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to P. palmivora. Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against Phytophthora spp. in cacao. IMPORTANCE Up to 40% of the world's cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research.
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Affiliation(s)
| | - Alina S. Puig
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, Frederick, Maryland, USA
| | | | - Emily E. Pfeufer
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, Frederick, Maryland, USA
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Tang T, Wang F, Fang G, Mao T, Guo J, Kuang H, Sun G, Guo X, Duan Y, You J. Coptischinensis Franch root rot infection disrupts microecological balance of rhizosphere soil and endophytic microbiomes. Front Microbiol 2023; 14:1180368. [PMID: 37303806 PMCID: PMC10248259 DOI: 10.3389/fmicb.2023.1180368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/21/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health. Coptis chinensis is one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms of C. chinensis. But the effects of root rot infection on rhizosphere microecological balance of C. chinensis have received little attention. Methods In this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity of C. chinensis by root rot. Results The results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples of C. chinensis than on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples of C. chinensis, which may also be one of the reasons for the serious root rot of C. chinensis. Discussion In conclusion, our findings suggested that root rot infection with C. chinensis disrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control of C. chinensis root rot by microecological regulation.
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Affiliation(s)
- Tao Tang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Fanfan Wang
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Guobin Fang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | - Ting Mao
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Jie Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Hui Kuang
- Hubei Provincial Plant Protection Station, Wuhan, China
| | | | - Xiaoliang Guo
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
| | - Yuanyuan Duan
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
| | - Jingmao You
- Key Laboratory of Chinese Herbal Medicine Biology and Cultivation, Ministry of Agriculture and Rural Affairs, Institute of Chinese Herbal Medicine, Hubei Academy of Agricultural Science, Enshi, China
- Hubei Engineering Research Center of Good Agricultural Practices (GAP) Production for Chinese Herbal Medicines, Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, China
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Bilous S, Likhanov A, Boroday V, Marchuk Y, Zelena L, Subin O, Bilous A. Antifungal Activity and Effect of Plant-Associated Bacteria on Phenolic Synthesis of Quercus robur L. PLANTS (BASEL, SWITZERLAND) 2023; 12:1352. [PMID: 36987039 PMCID: PMC10059881 DOI: 10.3390/plants12061352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of Quercus robur L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: Bacillus amyloliquefaciens, Bacillus subtilis, Delftia acidovorans, and Lelliottia amnigena. Determining the activity of pectolytic enzymes showed that the isolates B. subtilis and B. amyloliquefaciens could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely Fusarium tricinctum, Botrytis cinerea, and Sclerotinia sclerotiorum. Inoculation of B. subtilis, B. amyloliquefaciens, and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria Pectobacterium and Pseudomonas caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of Bacillus amyloliquefaciens and Bacillus subtilis isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus Bacillus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.
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Affiliation(s)
- Svitlana Bilous
- Education and Research Institute of Forestry and Landscape-Park Management, National University of Life and Environmental Sciences of Ukraine, 03041 Kyiv, Ukraine (Y.M.)
- Institute for Evolutionary Ecology NAS of Ukraine, 37 Lebedeva Str., 03143 Kiev, Ukraine
- Forestry Department, Weihenstephan-Triesdorf University of Applied Sciences, Germany, Hans-Carl-von-Carlowitz-Platz 3, 85354 Freising, Germany
| | - Artur Likhanov
- Education and Research Institute of Forestry and Landscape-Park Management, National University of Life and Environmental Sciences of Ukraine, 03041 Kyiv, Ukraine (Y.M.)
- Institute for Evolutionary Ecology NAS of Ukraine, 37 Lebedeva Str., 03143 Kiev, Ukraine
| | - Vira Boroday
- Education and Research Institute of Forestry and Landscape-Park Management, National University of Life and Environmental Sciences of Ukraine, 03041 Kyiv, Ukraine (Y.M.)
| | - Yurii Marchuk
- Education and Research Institute of Forestry and Landscape-Park Management, National University of Life and Environmental Sciences of Ukraine, 03041 Kyiv, Ukraine (Y.M.)
| | - Liubov Zelena
- Danylo Zabolotny Institute of Microbiology and Virology National Academy of Sciences of Ukraine, 154 Zabolotnogo Str., 03143 Kyiv, Ukraine
| | - Oleksandr Subin
- State Enterprise “State Centre of Agricultural Products Certification and Examination”, Janusha Korchaka Str. 9/12, 03143 Kyiv, Ukraine
| | - Andrii Bilous
- Education and Research Institute of Forestry and Landscape-Park Management, National University of Life and Environmental Sciences of Ukraine, 03041 Kyiv, Ukraine (Y.M.)
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Younginger BS, Stewart NU, Balkan MA, Ballhorn DJ. Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favouring a dominant fungus. Mol Ecol 2023; 32:244-257. [PMID: 36218009 DOI: 10.1111/mec.16732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed in vitro competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously undescribed endophyte appears to abundantly colonize the host to the detriment of other microfungi. Competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, and inoculation onto sterile fern gametophytes did not alter growth compared to sterile controls, suggesting its effects are not antagonistic. The presence of this endophyte in the fern population probably demonstrates a case of repeated colonization driving competitive exclusion of other fungal community members.
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Affiliation(s)
| | - Nathan U Stewart
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Mehmet A Balkan
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Daniel J Ballhorn
- Department of Biology, Portland State University, Portland, Oregon, USA
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Busby PE, Newcombe G, Neat AS, Averill C. Facilitating Reforestation Through the Plant Microbiome: Perspectives from the Phyllosphere. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:337-356. [PMID: 35584884 DOI: 10.1146/annurev-phyto-021320-010717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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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10
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A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes. Proc Natl Acad Sci U S A 2022; 119:e2204146119. [PMID: 35960845 PMCID: PMC9388140 DOI: 10.1073/pnas.2204146119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because microbiome research generally focuses on a single host or habitat, we know comparatively little about the diversity and distribution of microbiomes at a landscape scale. Our study demonstrates that most of the microbial diversity present within a watershed is maintained within environmental substrates like soil or stream water, and microbiomes of organisms are generally subsets of those that are lower on the food chain. This result challenges the notion that sources of microbial inoculum are likeliest derived from close relatives. By identifying sources of shared microbial diversity within the landscape, we can better understand the origins and assembly processes of symbiotic microbes and how this might abet global conservation, restoration, or bio-engineering goals, such as preserving biodiversity and ecosystem services. Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts’ microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.
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Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. THE ISME JOURNAL 2022; 16:1376-1387. [PMID: 35022514 PMCID: PMC9038669 DOI: 10.1038/s41396-021-01184-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 01/04/2023]
Abstract
Microbial communities associated with plant leaf surfaces (i.e., the phyllosphere) are increasingly recognized for their role in plant health. While accumulating evidence suggests a role for host filtering of its microbiota, far less is known about how community composition is shaped by dispersal, including from neighboring plants. We experimentally manipulated the local plant neighborhood within which tomato, pepper, or bean plants were grown in a 3-month field trial. Focal plants were grown in the presence of con- or hetero-specific neighbors (or no neighbors) in a fully factorial combination. At 30-day intervals, focal plants were harvested and replaced with a new age- and species-matched cohort while allowing neighborhood plants to continue growing. Bacterial community profiling revealed that the strength of host filtering effects (i.e., interspecific differences in composition) decreased over time. In contrast, the strength of neighborhood effects increased over time, suggesting dispersal from neighboring plants becomes more important as neighboring plant biomass increases. We next implemented a cross-inoculation study in the greenhouse using inoculum generated from the field plants to directly test host filtering of microbiomes while controlling for directionality and source of dispersal. This experiment further demonstrated that focal host species, the host from which the microbiome came, and in one case the donor hosts' neighbors, contribute to variation in phyllosphere bacterial composition. Overall, our results suggest that local dispersal is a key factor in phyllosphere assembly, and that demographic factors such as nearby neighbor identity and biomass or age are important determinants of phyllosphere microbiome diversity.
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12
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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] [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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13
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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. THE ISME JOURNAL 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] [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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14
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Christian N, Espino Basurto B, Toussaint A, Xu X, Ainsworth EA, Busby PE, Heath KD. Elevated carbon dioxide reduces a common soybean leaf endophyte. GLOBAL CHANGE BIOLOGY 2021; 27:4154-4168. [PMID: 34022078 DOI: 10.1111/gcb.15716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2 ] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2 ] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, KY, USA
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Baldemar Espino Basurto
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Amber Toussaint
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Xinyan Xu
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Elizabeth A Ainsworth
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Katy D Heath
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
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15
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Martínez-Arias C, Sobrino-Plata J, Gil L, Rodríguez-Calcerrada J, Martín JA. Priming of Plant Defenses against Ophiostoma novo-ulmi by Elm ( Ulmus minor Mill.) Fungal Endophytes. J Fungi (Basel) 2021; 7:687. [PMID: 34575725 PMCID: PMC8469682 DOI: 10.3390/jof7090687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 11/28/2022] Open
Abstract
Some fungal endophytes of forest trees are recognized as beneficial symbionts against stresses. In previous works, two elm endophytes from the classes Cystobasidiomycetes and Eurotiomycetes promoted host resistance to abiotic stress, and another elm endophyte from Dothideomycetes enhanced host resistance to Dutch elm disease (DED). Here, we hypothesize that the combined effect of these endophytes activate the plant immune and/or antioxidant system, leading to a defense priming and/or increased oxidative protection when exposed to the DED pathogen Ophiostoma novo-ulmi. To test this hypothesis, the short-term defense gene activation and antioxidant response were evaluated in DED-susceptible (MDV1) and DED-resistant (VAD2 and MDV2.3) Ulmus minor genotypes inoculated with O. novo-ulmi, as well as two weeks earlier with a mixture of the above-mentioned endophytes. Endophyte inoculation induced a generalized transient defense activation mediated primarily by salicylic acid (SA). Subsequent pathogen inoculation resulted in a primed defense response of variable intensity among genotypes. Genotypes MDV1 and VAD2 displayed a defense priming driven by SA, jasmonic acid (JA), and ethylene (ET), causing a reduced pathogen spread in MDV1. Meanwhile, the genotype MDV2.3 showed lower defense priming but a stronger and earlier antioxidant response. The defense priming stimulated by elm fungal endophytes broadens our current knowledge of the ecological functions of endophytic fungi in forest trees and opens new prospects for their use in the biocontrol of plant diseases.
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Affiliation(s)
- Clara Martínez-Arias
- Departamento de Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, 28040 Madrid, Spain; (J.S.-P.); (L.G.); (J.R.-C.); (J.A.M.)
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16
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Restoration of the mycobiome of the endangered Hawaiian mint Phyllostegia kaalaensis increases its resistance to a common powdery mildew. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Observations on the Potential of an Endophytic Fungus Associated with Cacao Leaves against Phytophthora palmivora. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12030037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A study was conducted to test the pathogenicity of an endophytic fungus associated with asymptomatic cacao leaves, to determine its identity through cultural, morphological and molecular characterization, and to evaluate itsantagonistic ability vs. Phytophthora palmivora causing cacao black pod rot disease. Experiments were carried out under laboratory and shade house conditions. Homogeneity of variances and normal data distribution were determined using Bartlett’s and Shapiro–Wilk tests, respectively. Inoculation of the endophyte in healthy cacao seedlings and pods at 5 × 105 to 1 × 106 conidia per mL by spraying resulted in asymptomatic infections. The endophyte was recovered from artificially inoculated tissues 14 and 26 days after inoculation (DAI) (UF18 seedlings), and at 10 (K9 seedlings) and 14 DAI from cacao pods. The endophyte was identified as Colletotrichum siamense based on its cultural, morphological and molecular characteristics. In vitroanti-pathogen assays showed that C. siamense had the potential to limit pathogen growth by antibiosis. At 3, 5 and 7 days after incubation period (DAIP), growth of the pathogen in co-cultivation with the endophyte measured 60.0, 70.0 and 71.0 mm, respectively, which wasconsiderably lower than the growth of the pathogen alone.
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18
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Fort T, Pauvert C, Zanne AE, Ovaskainen O, Caignard T, Barret M, Compant S, Hampe A, Delzon S, Vacher C. Maternal effects shape the seed mycobiome in Quercus petraea. THE NEW PHYTOLOGIST 2021; 230:1594-1608. [PMID: 33341934 DOI: 10.1111/nph.17153] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.
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Affiliation(s)
- Tania Fort
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
| | | | - Amy E Zanne
- Department of Biological Sciences, George Washington University, 800 22nd St., Washington, DC, 20052, USA
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, PO Box 65, Helsinki, 00014, Finland
- Center for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Matthieu Barret
- INRAE, IRHS, SFR 4207 QuaSaV, Institut Agro, Univ. Angers, Angers, 49000, France
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, Tulln, 3430, Austria
| | - Arndt Hampe
- INRAE, BIOGECO, Univ. Bordeaux, Pessac, 33615, France
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19
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U'Ren JM, Zimmerman NB. Oaks provide new perspective on seed microbiome assembly. THE NEW PHYTOLOGIST 2021; 230:1293-1295. [PMID: 33855719 DOI: 10.1111/nph.17305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Jana M U'Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Naupaka B Zimmerman
- Department of Biology, University of San Francisco, San Francisco, CA, 94117, USA
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20
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Herrmann M, Geesink P, Richter R, Küsel K. Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest. MICROBIAL ECOLOGY 2021; 81:157-168. [PMID: 32761502 PMCID: PMC7794210 DOI: 10.1007/s00248-020-01565-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/27/2020] [Indexed: 05/17/2023]
Abstract
The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.
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Affiliation(s)
- Martina Herrmann
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Patricia Geesink
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
| | - Ronny Richter
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Systematic Botany and Functional Biodiversity, Institute for Biology, Leipzig University, Johannisallee 21, 04103, Leipzig, Germany
- Geoinformatics and Remote Sensing, Institute of Geography, Leipzig University, Johannisallee 19a, 04103, Leipzig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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21
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Henning JA, Kinkel L, May G, Lumibao CY, Seabloom EW, Borer ET. Plant diversity and litter accumulation mediate the loss of foliar endophyte fungal richness following nutrient addition. Ecology 2020; 102:e03210. [PMID: 32981067 DOI: 10.1002/ecy.3210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 01/20/2023]
Abstract
Foliar fungal endophytes are ubiquitous plant symbionts that can affect plant growth and reproduction via their roles in pathogen and stress tolerance, as well as plant hormonal signaling. Despite their importance, we have a limited understanding of how foliar fungal endophytes respond to varying environmental conditions such as nutrient inputs. The responses of foliar fungal endophyte communities to increased nutrient deposition may be mediated by the simultaneous effects on within-host competition as well as the indirect impacts of altered host population size, plant productivity, and plant community diversity and composition. Here, we leveraged a 7-yr experiment manipulating nitrogen, phosphorus, potassium, and micronutrients to investigate how nutrient-induced changes to plant diversity, plant productivity, and plant community composition relate to changes in foliar fungal endophyte diversity and richness in a focal native grass host, Andropogon gerardii. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition. Thus, the effects of global change drivers, such as nutrient deposition, on characteristics of host populations and the diversity of their local communities are important for predicting the response of symbiont communities in a changing global environment.
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Affiliation(s)
- Jeremiah A Henning
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA.,Department of Biology, University of South Alabama, 5871 USA Drive N., Room 124, Mobile, Alabama, 36688, USA
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Candice Y Lumibao
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA.,Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
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22
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Rudgers JA, Afkhami ME, Bell-Dereske L, Chung YA, Crawford KM, Kivlin SN, Mann MA, Nuñez MA. Climate Disruption of Plant-Microbe Interactions. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-090819] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interactions between plants and microbes have important influences on evolutionary processes, population dynamics, community structure, and ecosystem function. We review the literature to document how climate change may disrupt these ecological interactions and develop a conceptual framework to integrate the pathways of plant-microbe responses to climate over different scales in space and time. We then create a blueprint to aid generalization that categorizes climate effects into changes in the context dependency of plant-microbe pairs, temporal mismatches and altered feedbacks over time, or spatial mismatches that accompany species range shifts. We pair a new graphical model of how plant-microbe interactions influence resistance to climate change with a statistical approach to predictthe consequences of increasing variability in climate. Finally, we suggest pathways through which plant-microbe interactions can affect resilience during recovery from climate disruption. Throughout, we take a forward-looking perspective, highlighting knowledge gaps and directions for future research.
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Affiliation(s)
- Jennifer A. Rudgers
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;,
| | - Michelle E. Afkhami
- Department of Biology, University of Miami, Coral Gables, Florida 33157, USA
| | - Lukas Bell-Dereske
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan 49060, USA
| | - Y. Anny Chung
- Departments of Plant Biology and Plant Pathology, University of Georgia, Athens, Georgia 30602, USA
| | - Kerri M. Crawford
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - Stephanie N. Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Michael A. Mann
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA;,
| | - Martin A. Nuñez
- Grupo de Ecología de Invasiones, Instituto de Investigaciones en Biodiversidad y Medioambiente, CONICET/Universidad Nacional del Comahue, Bariloche 8400, Argentina
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23
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24
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Harrison JG, Griffin EA. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol 2020. [PMID: 32115818 DOI: 10.1111/1462-2929.14968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.
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Affiliation(s)
- Joshua G Harrison
- Department of Botany, University of Wyoming, 3165, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Eric A Griffin
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, 87701, USA
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25
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Schroeder JW, Dobson A, Mangan SA, Petticord DF, Herre EA. Mutualist and pathogen traits interact to affect plant community structure in a spatially explicit model. Nat Commun 2020; 11:2204. [PMID: 32371877 PMCID: PMC7200732 DOI: 10.1038/s41467-020-16047-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023] Open
Abstract
Empirical studies show that plant-soil feedbacks (PSF) can generate negative density dependent (NDD) recruitment capable of maintaining plant community diversity at landscape scales. However, the observation that common plants often exhibit relatively weaker NDD than rare plants at local scales is difficult to reconcile with the maintenance of overall plant diversity. We develop a spatially explicit simulation model that tracks the community dynamics of microbial mutualists, pathogens, and their plant hosts. We find that net PSF effects vary as a function of both host abundance and key microbial traits (e.g., host affinity) in ways that are compatible with both common plants exhibiting relatively weaker local NDD, while promoting overall species diversity. The model generates a series of testable predictions linking key microbial traits and the relative abundance of host species, to the strength and scale of PSF and overall plant community diversity.
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Affiliation(s)
- John W Schroeder
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama.
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Andrew Dobson
- Princeton University, Princeton, NJ, USA
- Santa Fe Institute, Hyde Park Road, Santa Fe, NM, USA
| | - Scott A Mangan
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
- Washington University, St. Louis, MO, USA
| | - Daniel F Petticord
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Balboa Ancon, Republic of Panama
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Chen L, Swenson NG, Ji N, Mi X, Ren H, Guo L, Ma K. Differential soil fungus accumulation and density dependence of trees in a subtropical forest. Science 2020; 366:124-128. [PMID: 31604314 DOI: 10.1126/science.aau1361] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 01/02/2023]
Abstract
The mechanisms underlying interspecific variation in conspecific negative density dependence (CNDD) are poorly understood. Using a multilevel modeling approach, we combined long-term seedling demographic data from a subtropical forest plot with soil fungal community data by means of DNA sequencing to address the feedback of various guilds of soil fungi on the density dependence of trees. We show that mycorrhizal type mediates tree neighborhood interactions at the community level, and much of the interspecific variation in CNDD is explained by how tree species differ in their fungal density accumulation rates as they grow. Species with higher accumulation rates of pathogenic fungi suffered more from CNDD, whereas species with lower CNDD had higher accumulation rates of ectomycorrhizal fungi, suggesting that mutualistic and pathogenic fungi play important but opposing roles.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Nathan G Swenson
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Niuniu Ji
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Haibao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Harrison JG, Griffin EA. The diversity and distribution of endophytes across biomes, plant phylogeny and host tissues: how far have we come and where do we go from here? Environ Microbiol 2020; 22:2107-2123. [PMID: 32115818 DOI: 10.1111/1462-2920.14968] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 12/18/2022]
Abstract
The interiors of plants are colonized by diverse microorganisms that are referred to as endophytes. Endophytes have received much attention over the past few decades, yet many questions remain unanswered regarding patterns in their biodiversity at local to global scales. To characterize research effort to date, we synthesized results from ~600 published studies. Our survey revealed a global research interest and highlighted several gaps in knowledge. For instance, of the 17 biomes encompassed by our survey, 7 were understudied and together composed only 7% of the studies that we considered. We found that fungal endophyte diversity has been characterized in at least one host from 30% of embryophyte families, while bacterial endophytes have been surveyed in hosts from only 10.5% of families. We complimented our survey with a vote counting procedure to determine endophyte richness patterns among plant tissue types. We found that variation in endophyte assemblages in above-ground tissues varied with host growth habit. Stems were the richest tissue in woody plants, whereas roots were the richest tissue in graminoids. For forbs, we found no consistent differences in relative tissue richness among studies. We propose future directions to fill the gaps in knowledge we uncovered and inspire further research.
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Affiliation(s)
- Joshua G Harrison
- Department of Botany, University of Wyoming, 3165, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Eric A Griffin
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, 87701, USA
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Christian N, Sedio BE, Florez-Buitrago X, Ramírez-Camejo LA, Rojas EI, Mejía LC, Palmedo S, Rose A, Schroeder JW, Herre EA. Host affinity of endophytic fungi and the potential for reciprocal interactions involving host secondary chemistry. AMERICAN JOURNAL OF BOTANY 2020; 107:219-228. [PMID: 32072625 DOI: 10.1002/ajb2.1436] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/23/2019] [Indexed: 05/20/2023]
Abstract
PREMISE Interactions between fungal endophytes and their host plants present useful systems for identifying important factors affecting assembly of host-associated microbiomes. Here we investigated the role of secondary chemistry in mediating host affinity of asymptomatic foliar endophytic fungi using Psychotria spp. and Theobroma cacao (cacao) as hosts. METHODS First, we surveyed endophytic communities in Psychotria species in a natural common garden using culture-based methods. Then we compared differences in endophytic community composition with differences in foliar secondary chemistry in the same host species, determined by liquid chromatography-tandem mass spectrometry. Finally, we tested how inoculation with live and heat-killed endophytes affected the cacao chemical profile. RESULTS Despite sharing a common environment and source pool for endophyte spores, different Psychotria host species harbored strikingly different endophytic communities that reflected intrinsic differences in their leaf chemical profiles. In T. cacao, inoculation with live and heat-killed endophytes produced distinct cacao chemical profiles not found in uninoculated plants or pure fungal cultures, suggesting that endophytes, like pathogens, induce changes in secondary chemical profiles of their host plant. CONCLUSIONS Collectively our results suggest at least two potential processes: (1) Plant secondary chemistry influences assembly and composition of fungal endophytic communities, and (2) host colonization by endophytes subsequently induces changes in the host chemical landscape. We propose a series of testable predictions based on the possibility that reciprocal chemical interactions are a general property of plant-endophyte interactions.
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Affiliation(s)
- Natalie Christian
- Department of Plant Biology, School of Integrative Biology, University of Illinois, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
- Department of Biology, University of Louisville, 139 Life Sciences Bldg., Louisville, KY, 40208, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO AA 34002-9998, USA
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Apartado 0843-01103, Ciudad del Saber, Ancón, Republic of Panama
- Department of Integrative Biology, University of Texas at Austin, 2415 Speedway #C0930, Austin, TX, 78712, USA
| | | | - Luis A Ramírez-Camejo
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Apartado 0843-01103, Ciudad del Saber, Ancón, Republic of Panama
- Department of Botany and Plant Pathology, Purdue University, 915 W. State St., West Lafayette, IN, 47907, USA
| | - Enith I Rojas
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO AA 34002-9998, USA
| | - Luis C Mejía
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Apartado 0843-01103, Ciudad del Saber, Ancón, Republic of Panama
| | - Sage Palmedo
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Ln., Princeton, NJ, 08544, USA
| | - Autumn Rose
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Ln., Princeton, NJ, 08544, USA
| | - John W Schroeder
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO AA 34002-9998, USA
- Ecology, Evolution, and Marine Biology, University of California Santa-Barbara, Noble Hall 2116, Santa Barbara, CA, 93106, USA
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, DPO AA 34002-9998, USA
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Heath KD, Podowski JC, Heniff S, Klinger CR, Burke PV, Weese DJ, Yang WH, Lau JA. Light availability and rhizobium variation interactively mediate the outcomes of legume-rhizobium symbiosis. AMERICAN JOURNAL OF BOTANY 2020; 107:229-238. [PMID: 32072629 DOI: 10.1002/ajb2.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/08/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Nutrients, light, water, and temperature are key factors limiting the growth of individual plants in nature. Mutualistic interactions between plants and microbes often mediate resource limitation for both partners. In the mutualism between legumes and rhizobia, plants provide rhizobia with carbon in exchange for fixed nitrogen. Because partner quality in mutualisms is genotype-dependent, within-species genetic variation is expected to alter the responses of mutualists to changes in the resource environment. Here we ask whether partner quality variation in rhizobia mediates the response of host plants to changing light availability, and conversely, whether light alters the expression of partner quality variation. METHODS We inoculated clover hosts with 11 strains of Rhizobium leguminosarum that differed in partner quality, grew plants under either ambient or low light conditions in the greenhouse, and measured plant growth, nodule traits, and foliar nutrient composition. RESULTS Light availability and rhizobium inoculum interactively determined plant growth, and variation in rhizobium partner quality was more apparent in ambient light. CONCLUSIONS Our results suggest that variation in the costs and benefits of rhizobium symbionts mediate host responses to light availability and that rhizobium strain variation might more important in higher-light environments. Our work adds to a growing appreciation for the role of microbial intraspecific and interspecific diversity in mediating extended phenotypes in their hosts and suggests an important role for light availability in the ecology and evolution of legume-rhizobium symbiosis.
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Affiliation(s)
- Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Justin C Podowski
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Stephanie Heniff
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Christie R Klinger
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Patricia V Burke
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Dylan J Weese
- Department of Biology, St. Ambrose University, Davenport, IA, 52803, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
| | - Jennifer A Lau
- W. K. Kellogg Biological Station and Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Affiliation(s)
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | | | - Sasha G. Tetu
- Department of Molecular Sciences Macquarie University North Ryde NSW Australia
| | - Michael R. Gillings
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
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Fang K, Miao YF, Chen L, Zhou J, Yang ZP, Dong XF, Zhang HB. Tissue-Specific and Geographical Variation in Endophytic Fungi of Ageratina adenophora and Fungal Associations With the Environment. Front Microbiol 2019; 10:2919. [PMID: 31921082 PMCID: PMC6930192 DOI: 10.3389/fmicb.2019.02919] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022] Open
Abstract
To understand the distribution of the cultivable fungal community in plant tissues and the associations of these fungi with their surrounding environments during the geographical expansion of an invasive plant, Ageratina adenophora, we isolated the cultivable fungi from 72 plant tissues, 12 soils, and 12 air samples collected from six areas in Yunnan Province, China. A total of 4066 isolates were investigated, including 1641 endophytic fungi, 233 withered leaf fungi, 1255 fungi from air, and 937 fungi from soil. These fungi were divided into 458 and 201 operational taxonomic units (OTUs) with unique and 97% ITS gene sequence identity, respectively. Phylogenetic analysis showed that the fungi belonged to four phyla, including Ascomycota (94.20%), Basidiomycota (2.71%), Mortierellomycota (3.03%), and Mucoromycota (0.07%). The dominant genera of cultivable endophytic fungi were Colletotrichum (34.61%), Diaporthe (17.24%), Allophoma (8.03%), and Fusarium (4.44%). Colletotrichum and Diaporthe were primarily isolated from mature leaves, Allophoma from stems, and Fusarium from roots, indicating that the enrichment of endophytic fungi is tissue-specific and fungi rarely grew systemically within A. adenophora. In the surrounding environment, Alternaria (21.46%), Allophoma (19.31%), Xylaria (18.45%), and Didymella (18.03%) were dominant in the withered leaves, Cladosporium (22.86%), Trichoderma (14.27%), and Epicoccum (9.83%) were dominant in the canopy air, and Trichoderma (27.27%) and Mortierella (20.46%) were dominant in the rhizosphere soils. Further analysis revealed that the cultivable endophytic fungi changed across geographic areas and showed a certain degree of variation in different tissues of A. adenophora. The cultivable fungi in mature and withered leaves fluctuated more than those in roots and stems. We also found that some cultivable endophytic fungi might undergo tissue-to-tissue migration and that the stem could be a transport tissue by which airborne fungi infect roots. Finally, we provided evidence that the fungal community within A. adenophora was partially shared with the contiguous environment. The data suggested a frequent interaction between fungi associated with A. adenophora and those in surrounding environments, reflecting a compromise driven by both functional requirements for plant growth and local environmental conditions.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yi-Fang Miao
- Lu Cheng Center for Disease Control and Prevention, Changzhi, China
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Zhi-Ping Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
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Fang K, Chen L, Zhou J, Yang ZP, Dong XF, Zhang HB. Plant-soil-foliage feedbacks on seed germination and seedling growth of the invasive plant Ageratina adenophora. Proc Biol Sci 2019; 286:20191520. [PMID: 31822255 DOI: 10.1098/rspb.2019.1520] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Some exotic plants become invasive because they partially release from soil-borne enemies and thus benefit from positive plant-soil feedbacks (PSFs) in the introduced range. However, reports that have focused only on PSFs may exaggerate the invader's competitiveness. Here, we conducted three experiments to characterize plant-soil-foliage feedbacks, including mature leaves (ML), leaf litter (LL), rhizosphere soil (RS) and leaves plus soil (LS), on the early growth stages of the invasive plant Ageratina adenophora. In general, the feedbacks from aboveground (ML, LL) adversely affected A. adenophora by delaying germination time, inhibiting germination rate and reducing seedling growth. The increased invasion history exacerbated the adverse effects of LL and LS feedbacks on seedling growth. These adverse effects were partially contributed by more abundant fungi (e.g. Didymella) or/and more virulent fungi (e.g. Fusarium) developed in the aboveground part of A. adenophora during the invasion. Interestingly, the aboveground adverse effects can be weakened by microbes from RSs. Our novel findings emphasize the important role of aboveground feedbacks in the evaluation of plant invasiveness, and their commonness and significance remain to be explored in other invasive systems.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China.,School of Ecology and Environmental Science, Yunnan University, Kunming 650091, People's Republic of China
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China.,School of Ecology and Environmental Science, Yunnan University, Kunming 650091, People's Republic of China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Zhi-Ping Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, People's Republic of China.,School of Life Sciences, Yunnan University, Kunming 650091, People's Republic of China.,School of Ecology and Environmental Science, Yunnan University, Kunming 650091, People's Republic of China
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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment. DIVERSITY 2019. [DOI: 10.3390/d11120234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.
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Kosawang C, Sørensen H, Kjær ED, Dilokpimol A, McKinney LV, Collinge DB, Nielsen LR. Defining the twig fungal communities of Fraxinus species and Fraxinus excelsior genotypes with differences in susceptibility to ash dieback. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies. The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. This Perspective article outlines research priorities to strengthen our current knowledge of host-microbiome interactions, to help predict responses to anthropogenic stressors and to inform future management strategies.
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Decreased Root-Knot Nematode Gall Formation in Roots of the Morning Glory Ipomoea tricolor Symbiotic with Ergot Alkaloid-Producing Fungal Periglandula Sp. J Chem Ecol 2019; 45:879-887. [PMID: 31686336 DOI: 10.1007/s10886-019-01109-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Many species of morning glories (Convolvulaceae) form symbioses with seed-transmitted Periglandula fungal endosymbionts, which produce ergot alkaloids and may contribute to defensive mutualism. Allocation of seed-borne ergot alkaloids to various tissues of several Ipomoea species has been demonstrated, including roots of I. tricolor. The goal of this study was to determine if infection of I. tricolor by the Periglandula sp. endosymbiont affects Southern root-knot nematode (Meloidogyne incognita) gall formation and host plant biomass. We hypothesized that I. tricolor plants infected by Periglandula (E+) would develop fewer nematode-induced galls compared to non-symbiotic plants (E-). E+ or E- status of plant lines was confirmed by testing methanol extracts from individual seeds for endosymbiont-produced ergot alkaloids. To test the effects of Periglandula on nematode colonization, E+ and E- I. tricolor seedlings were grown in soil infested with high densities of M. incognita nematodes (N+) or no nematodes (N-) for four weeks in the greenhouse before harvesting. After harvest, nematode colonization of roots was visualized microscopically, and total gall number and plant biomass were quantified. Four ergot alkaloids were detected in roots of E+ plants, but no alkaloids were found in E- plants. Gall formation was reduced by 50% in E+ plants compared to E- plants, independent of root biomass. Both N+ plants and E+ plants had significantly reduced biomass compared to N- and E- plants, respectively. These results demonstrate Periglandula's defensive role against biotic enemies, albeit with a potential trade-off with host plant growth.
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Lumibao CY, Borer ET, Condon B, Kinkel L, May G, Seabloom EW. Site-specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales. Ecol Evol 2019; 9:12231-12244. [PMID: 31832156 PMCID: PMC6854330 DOI: 10.1002/ece3.5711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 12/14/2022] Open
Abstract
The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within-host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.
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Affiliation(s)
- Candice Y. Lumibao
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Elizabeth T. Borer
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Bradford Condon
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Linda Kinkel
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMinnesota
| | - Georgiana May
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
| | - Eric W. Seabloom
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt. PaulMinnesota
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Christian N, Herre EA, Clay K. Foliar endophytic fungi alter patterns of nitrogen uptake and distribution in Theobroma cacao. THE NEW PHYTOLOGIST 2019; 222:1573-1583. [PMID: 30664252 DOI: 10.1111/nph.15693] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/14/2019] [Indexed: 05/20/2023]
Abstract
Colonization by foliar endophytic fungi can affect the expression of host plant defenses and other ecologically important traits. However, whether endophyte colonization affects the uptake or redistribution of resources within and among host plant tissues remains unstudied. We inoculated leaves of Theobroma cacao with four common colonizers that range in their effect from protective to pathogenic (Colletotrichum tropicale, Pestalotiopsis sp., Colletotrichum theobromicola, or Phytophthora palmivora). We pulsed the soil with nitrogen-15 (15 N) and then traced 15 N uptake and its subsequent distribution to whole plants and individual leaves. At a whole-plant level, C. tropicale-inoculated plants showed significantly greater 15 N uptake than endophyte-free plants did in the same pot. Among leaves within plants, younger leaves were particularly enriched in 15 N, but endophyte inoculation at the individual leaf level did not alter 15 N distribution within plants. However, leaves co-inoculated with pathogenic Phytophthora and protective C. tropicale experienced significantly elevated 15 N content as pathogen damage increased, compared with leaves inoculated only with the pathogen. Further, endophyte-pathogen co-infection also increased total plant biomass. Our results indicate that colonization by foliar endophytes significantly affects N uptake and distribution among and within host plants in ways that appear to be context dependent on other microbiome components.
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Affiliation(s)
- Natalie Christian
- Department of Plant Biology, School of Integrative Biology, University of Illinois, 505 S. Goodwin Ave., Urbana, IL, 61801, USA
- Evolution, Ecology and Behavior Program, Department of Biology, Indiana University, 1001 E. 3rd St., Bloomington, IN, 47405, USA
| | - Edward Allen Herre
- Smithsonian Tropical Research Institute, Unit 9100 Box 0948, Miami, FL, 34002-9998, USA
| | - Keith Clay
- Evolution, Ecology and Behavior Program, Department of Biology, Indiana University, 1001 E. 3rd St., Bloomington, IN, 47405, USA
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St Charles Ave., New Orleans, LA, 70118, USA
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Forest Tree Microbiomes and Associated Fungal Endophytes: Functional Roles and Impact on Forest Health. FORESTS 2019. [DOI: 10.3390/f10010042] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Terrestrial plants including forest trees are generally known to live in close association with microbial organisms. The inherent features of this close association can be commensalism, parasitism or mutualism. The term “microbiota” has been used to describe this ecological community of plant-associated pathogenic, mutualistic, endophytic and commensal microorganisms. Many of these microbiota inhabiting forest trees could have a potential impact on the health of, and disease progression in, forest biomes. Comparatively, studies on forest tree microbiomes and their roles in mutualism and disease lag far behind parallel work on crop and human microbiome projects. Very recently, our understanding of plant and tree microbiomes has been enriched due to novel technological advances using metabarcoding, metagenomics, metatranscriptomics and metaproteomics approaches. In addition, the availability of massive DNA databases (e.g., NCBI (USA), EMBL (Europe), DDBJ (Japan), UNITE (Estonia)) as well as powerful computational and bioinformatics tools has helped to facilitate data mining by researchers across diverse disciplines. Available data demonstrate that plant phyllosphere bacterial communities are dominated by members of only a few phyla (Proteobacteria, Actinobacteria, Bacteroidetes). In bulk forest soil, the dominant fungal group is Basidiomycota, whereas Ascomycota is the most prevalent group within plant tissues. The current challenge, however, is how to harness and link the acquired knowledge on microbiomes for translational forest management. Among tree-associated microorganisms, endophytic fungal biota are attracting a lot of attention for their beneficial health- and growth-promoting effects, and were preferentially discussed in this review.
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Newcombe G, Harding A, Ridout M, Busby PE. A Hypothetical Bottleneck in the Plant Microbiome. Front Microbiol 2018; 9:1645. [PMID: 30108556 PMCID: PMC6080073 DOI: 10.3389/fmicb.2018.01645] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/02/2018] [Indexed: 01/22/2023] Open
Abstract
The plant microbiome may be bottlenecked at the level of endophytes of individual seeds. Strong defense of developing seeds is predicted by optimal defense theory, and we have experimentally demonstrated exclusionary interactions among endophytic microbes infecting individual seeds of Centaurea stoebe. Having found a single, PDA-culturable microbe per seed or none in an exploratory study with Centaurea stoebe, we completed a more extensive survey of an additional 98 plant species representing 39 families. We again found that individual, surface-sterilized seeds of all species hosted only one PDA-culturable bacterial or fungal endophyte per seed, or none. PDA-unculturables were not determined but we expect them to also be bottlenecked in individual seeds, as they too should be governed by exclusionary interactions. If the bottleneck were confirmed with high-throughput sequencing of individual seeds then it would make sense to further investigate the Primary Symbiont Hypothesis (PSH). This includes the prediction that primary symbionts (i.e., the winners of the exclusionary battles among seed endophytes) have strong effects on seedlings depending on symbiont identity.
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Affiliation(s)
- George Newcombe
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, Moscow, ID, United States
| | - Abby Harding
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, Moscow, ID, United States
| | - Mary Ridout
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, Moscow, ID, United States
| | - Posy E. Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Griffin EA, Carson WP. Tree Endophytes: Cryptic Drivers of Tropical Forest Diversity. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Hillesland KL. Evolution on the bright side of life: microorganisms and the evolution of mutualism. Ann N Y Acad Sci 2017; 1422:88-103. [PMID: 29194650 DOI: 10.1111/nyas.13515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/05/2017] [Accepted: 09/11/2017] [Indexed: 01/15/2023]
Abstract
Mutualistic interactions, where two interacting species have a net beneficial effect on each other's fitness, play a crucial role in the survival and evolution of many species. Despite substantial empirical and theoretical work in past decades, the impact of these interactions on natural selection is not fully understood. In addition, mutualisms between microorganisms have been largely ignored, even though they are ecologically important and can be used as tools to bridge the gap between theory and empirical work. Here, I describe two problems with our current understanding of natural selection in mutualism and highlight the properties of microbial mutualisms that could help solve them. One problem is that bias and methodological problems have limited our understanding of the variety of mechanisms by which species may adapt to mutualism. Another problem is that it is rare for experiments testing coevolution in mutualism to address whether each species has adapted to evolutionary changes in its partner. These problems can be addressed with genome resequencing and time-shift experiments, techniques that are easier to perform in microorganisms. In addition, microbial mutualisms may inspire novel insights and hypotheses about natural selection in mutualism.
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