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Poma-Angamarca RA, Rojas JR, Sánchez-Rodríguez A, Ruiz-González MX. Diversity of Leaf Fungal Endophytes from Two Coffea arabica Varieties and Antagonism towards Coffee Leaf Rust. PLANTS (BASEL, SWITZERLAND) 2024; 13:814. [PMID: 38592839 PMCID: PMC11154406 DOI: 10.3390/plants13060814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Coffee has immense value as a worldwide-appreciated commodity. However, its production faces the effects of climate change and the spread of severe diseases such as coffee leaf rust (CLR). The exploration of fungal endophytes associated with Coffea sp. has already found the existence of nearly 600 fungal species, but their role in the plants remains practically unknown. We have researched the diversity of leaf fungal endophytes in two Coffea arabica varieties: one susceptible and one resistant to CLR. Then, we conducted cross-infection essays with four common endophyte species (three Colletotrichum sp. and Xylaria sp. 1) and Hemileia vastatrix (CLR) in leaf discs, to investigate the interaction of the endophytes on CLR colonisation success and severity of infection. Two Colletotrichum sp., when inoculated 72 h before H. vastatrix, prevented the colonisation of the leaf disc by the latter. Moreover, the presence of endophytes prior to the arrival of H. vastatrix ameliorated the severity of CLR. Our work highlights both the importance of characterising the hidden biodiversity of endophytes and investigating their potential roles in the plant-endophyte interaction.
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Affiliation(s)
- Ruth A. Poma-Angamarca
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Jacqueline R. Rojas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
| | - Mario X. Ruiz-González
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador; (R.A.P.-A.); (J.R.R.); (A.S.-R.)
- SENESCYT is the Secretaría de Educación Superior, Ciencia, Tecnología e Innovación from the Government of Ecuador, Proyecto Prometeo SENESCYT, Universidad Técnica Particular de Loja, San Cayetano Alto s/n, Loja 1101608, Ecuador
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U'Ren JM, Oita S, Lutzoni F, Miadlikowska J, Ball B, Carbone I, May G, Zimmerman NB, Valle D, Trouet V, Arnold AE. Environmental drivers and cryptic biodiversity hotspots define endophytes in Earth's largest terrestrial biome. Curr Biol 2024; 34:1148-1156.e7. [PMID: 38367618 DOI: 10.1016/j.cub.2024.01.063] [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: 05/29/2023] [Revised: 12/03/2023] [Accepted: 01/25/2024] [Indexed: 02/19/2024]
Abstract
Understanding how symbiotic associations differ across environmental gradients is key to predicting the fate of symbioses as environments change, and it is vital for detecting global reservoirs of symbiont biodiversity in a changing world.1,2,3 However, sampling of symbiotic partners at the full-biome scale is difficult and rare. As Earth's largest terrestrial biome, boreal forests influence carbon dynamics and climate regulation at a planetary scale. Plants and lichens in this biome host the highest known phylogenetic diversity of fungal endophytes, which occur within healthy photosynthetic tissues and can influence hosts' resilience to stress.4,5 We examined how communities of endophytes are structured across the climate gradient of the boreal biome, focusing on the dominant plant and lichen species occurring across the entire south-to-north span of the boreal zone in eastern North America. Although often invoked for understanding the distribution of biodiversity, neither a latitudinal gradient nor mid-domain effect5,6,7 can explain variation in endophyte diversity at this trans-biome scale. Instead, analyses considering shifts in forest characteristics, Picea biomass and age, and nutrients in host tissues from 46° to 58° N reveal strong and distinctive signatures of climate in defining endophyte assemblages in each host lineage. Host breadth of endophytes varies with climate factors, and biodiversity hotspots can be identified at plant-community transitions across the boreal zone at a global scale. Placed against a backdrop of global circumboreal sampling,4 our study reveals the sensitivity of endophytic fungi, their reservoirs of biodiversity, and their important symbiotic associations, to climate.
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Affiliation(s)
- Jana M U'Ren
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA
| | - Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Bernard Ball
- Department of Biology, Duke University, Durham, NC 27708, USA; School of Biology and Environmental Science, University College Dublin, Science Centre Belfield, Dublin D04 V1W8, Ireland
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Naupaka B Zimmerman
- Department of Biology, University of San Francisco, San Francisco, CA 94117, USA
| | - Denis Valle
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Valerie Trouet
- Laboratory of Tree Ring Research, University of Arizona, Tucson, AZ 85721, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Department of Ecology and Evolutionary Biology, BIO5 Institute, Ecosystem Genomics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85721, USA.
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Rétif F, Kunz C, Calabro K, Duval C, Prado S, Bailly C, Baudouin E. Seed fungal endophytes as biostimulants and biocontrol agents to improve seed performance. FRONTIERS IN PLANT SCIENCE 2023; 14:1260292. [PMID: 37941673 PMCID: PMC10628453 DOI: 10.3389/fpls.2023.1260292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
Seed germination is a major determinant of plant development and final yield establishment but strongly reliant on the plant's abiotic and biotic environment. In the context of global climate change, classical approaches to improve seed germination under challenging environments through selection and use of synthetic pesticides reached their limits. A currently underexplored way is to exploit the beneficial impact of the microorganisms associated with plants. Among plant microbiota, endophytes, which are micro-organisms living inside host plant tissues without causing any visible symptoms, are promising candidates for improving plant fitness. They possibly establish a mutualistic relationship with their host, leading to enhanced plant yield and improved tolerance to abiotic threats and pathogen attacks. The current view is that such beneficial association relies on chemical mediations using the large variety of molecules produced by endophytes. In contrast to leaf and root endophytes, seed-borne fungal endophytes have been poorly studied although they constitute the early-life plant microbiota. Moreover, seed-borne fungal microbiota and its metabolites appear as a pertinent lever for seed quality improvement. This review summarizes the recent advances in the identification of seed fungal endophytes and metabolites and their benefits for seed biology, especially under stress. It also addresses the mechanisms underlying fungal effects on seed physiology and their potential use to improve crop seed performance.'
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Affiliation(s)
- Félix Rétif
- Sorbonne Université, CNRS UMR7622, Institut de Biologie Paris-Seine-Laboratoire de Biologie du Développement (IBPS-LBD), Paris, France
| | - Caroline Kunz
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Paris, France
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927, Paris, France
| | - Kevin Calabro
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Paris, France
| | - Clémence Duval
- Seedlab, Novalliance, Zone Anjou Actiparc, Longué-Jumelles, France
| | - Soizic Prado
- Muséum National d’Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Paris, France
| | - Christophe Bailly
- Sorbonne Université, CNRS UMR7622, Institut de Biologie Paris-Seine-Laboratoire de Biologie du Développement (IBPS-LBD), Paris, France
| | - Emmanuel Baudouin
- Sorbonne Université, CNRS UMR7622, Institut de Biologie Paris-Seine-Laboratoire de Biologie du Développement (IBPS-LBD), Paris, France
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4
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The impact of polyphenolic compounds on the in vitro growth of oak-associated foliar endophytic and saprotrophic fungi. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Characterization of Seed Mycobiota Using Culture-Dependent and Culture-Independent Approaches. Methods Mol Biol 2022; 2605:65-78. [PMID: 36520389 DOI: 10.1007/978-1-0716-2871-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Seed fungi are potentially important for their roles in seedling microbiome assembly and seedling health, but surveys of full seed fungal communities remain limited. While culture-dependent methods have been used to characterize some members of the seed mycobiota, recent culture-independent studies have improved the ease in identifying and characterizing full seed fungal communities. In this chapter, we describe how to survey seed fungi using both traditional culture-based methods and culture-free metabarcoding. We first describe protocols for the isolation and long-term preservation of fungal strains from individual seeds and for the extraction and amplification of DNA from such fungal isolates for identification with Sanger sequencing. We also detail how to extract, amplify, and sequence fungal DNA directly from individual seeds. Finally, we provide suggestions for troubleshooting media choices, PCR inhibition by isolates and plant tissue, and PCR limitation by low fungal DNA.
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Tellez PH, Arnold AE, Leo AB, Kitajima K, Van Bael SA. Traits along the leaf economics spectrum are associated with communities of foliar endophytic symbionts. Front Microbiol 2022; 13:927780. [PMID: 35966664 PMCID: PMC9366602 DOI: 10.3389/fmicb.2022.927780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Leaf traits of plants worldwide are classified according to the Leaf Economics Spectrum (LES), which links leaf functional traits to evolutionary life history strategies. As a continuum ranging from thicker, tough leaves that are low in nitrogen (N) to thinner, softer, leaves that are high in N, the LES brings together physical, chemical, and ecological traits. Fungal endophytes are common foliar symbionts that occur in healthy, living leaves, especially in tropical forests. Their community composition often differs among co-occurring host species in ways that cannot be explained by environmental conditions or host phylogenetic relationships. Here, we tested the over-arching hypothesis that LES traits act as habitat filters that shape communities of endophytes both in terms of composition, and in terms of selecting for endophytes with particular suites of functional traits. We used culture-based and culture-free surveys to characterize foliar endophytes in mature leaves of 30 phylogenetically diverse plant species with divergent LES traits in lowland Panama, and then measured functional traits of dominant endophyte taxa in vitro. Endophytes were less abundant and less diverse in thick, tough, leaves compared to thin, softer, leaves in the same forest, even in closely related plants. Endophyte communities differed according to leaf traits, including leaf punch strength and carbon and nitrogen content. The most common endophyte taxa in leaves at different ends of the LES differ in their cellulase, protease, chitinase, and antipathogen activity. Our results extend the LES framework for the first time to diverse and ecologically important endophytes, opening new hypotheses regarding the degree to which foliar symbionts respond to, and extend, the functional traits of leaves they inhabit.
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Affiliation(s)
- Peter H Tellez
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Ashton B Leo
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Kaoru Kitajima
- Smithsonian Tropical Research Institute, Panama City, Panama
- Division of Forest and Biomaterial Science, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
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Bergmann GE, Leveau JHJ. A metacommunity ecology approach to understanding microbial community assembly in developing plant seeds. Front Microbiol 2022; 13:877519. [PMID: 35935241 PMCID: PMC9355165 DOI: 10.3389/fmicb.2022.877519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Microorganisms have the potential to affect plant seed germination and seedling fitness, ultimately impacting plant health and community dynamics. Because seed-associated microbiota are highly variable across individual plants, plant species, and environments, it is challenging to identify the dominant processes that underlie the assembly, composition, and influence of these communities. We propose here that metacommunity ecology provides a conceptually useful framework for studying the microbiota of developing seeds, by the application of metacommunity principles of filtering, species interactions, and dispersal at multiple scales. Many studies in seed microbial ecology already describe individual assembly processes in a pattern-based manner, such as correlating seed microbiome composition with genotype or tracking diversity metrics across treatments in dispersal limitation experiments. But we see a lot of opportunities to examine understudied aspects of seed microbiology, including trait-based research on mechanisms of filtering and dispersal at the micro-scale, the use of pollination exclusion experiments in macro-scale seed studies, and an in-depth evaluation of how these processes interact via priority effect experiments and joint species distribution modeling.
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Blaalid R, Davey ML. Habitat Protection Approaches Facilitate Conservation of Overlooked Fungal Diversity - A Case Study From the Norwegian Coastal Heathland System. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:886685. [PMID: 37746238 PMCID: PMC10512255 DOI: 10.3389/ffunb.2022.886685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 09/26/2023]
Abstract
European coastal heathlands are distinct ecosystems shaped by land use tradition and they have experienced an 80% area reduction from their historical maximum. These mosaics of mires and wind exposed patches have ericaceous shrub dominated vegetation, and soils within coastal heathlands are characterized by low pH and high levels of recalcitrant debris. Using a culture-based approach with molecular identification of isolates, we characterized root-associated fungal communities of six ericaceous species in eight heathland localities along Norway's western coast. Site-level alpha diversity ranged from 21-38 OTUs, while the total estimated gamma diversity for culturable heathland root fungi was 190-231 OTUs. Most species recovered are previously reported at low abundance in Norway, suggesting the biodiversity in this community is underreported, rather than novel for science. The fungi recovered were primarily Ascomycota, specifically endophytic Phialocephala, and Pezicula, and no host specificity was observed in the communities. The fungal communities exhibited high turnover and low nestedness, both between ericaceous hosts and across heathland sites. We observed no spatial patterns in fungal betadiversity, and this heterogeneity may be a product of the unique historic land use practices at each locality creating a distinct mycofloral "fingerprint". Robust diversity estimates will be key for managing fungal biodiversity in coastal heathlands. Our results indicate that sampling schemes that maximize the number of host plants sampled per site, rather than the number of cultures per plant yield improved alpha diversity estimates. Similarly, gamma diversity estimates are improved by maximizing the total number of localities sampled, rather than increasing the number of plants sampled per locality. We argue that while the current protected status of coastal heathland habitats and restoration efforts have knock-on effects for the conservation of fungal biodiversity, fungi have a vital functional role in the ecosystem and holistic conservation plans that consider fungal biodiversity would be beneficial.
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Affiliation(s)
- Rakel Blaalid
- Department of Natural History, University Museum of Bergen, Bergen, Norway
- Norwegian Institute for Nature Research, NINA Bergen, Bergen, Norway
| | - Marie L. Davey
- Norwegian Institute for Nature Research, Terrestrial Biodiversity Department, Trondheim, Norway
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9
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Bowman EA, Arnold AE. Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape. THE ISME JOURNAL 2021; 15:3437-3454. [PMID: 34099878 PMCID: PMC8630060 DOI: 10.1038/s41396-021-01006-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 07/30/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023]
Abstract
Fungal communities associated with plants often decrease in similarity as the distance between sampling sites increases (i.e., they demonstrate distance decay). In the southwestern USA, forests occur in highlands separated from one another by warmer, drier biomes with plant and fungal communities that differ from those at higher elevations. These disjunct forests are broadly similar in climate to one another, offering an opportunity to examine drivers of distance decay in plant-associated fungi across multiple ecologically similar yet geographically disparate landscapes. We examined ectomycorrhizal and foliar endophytic fungi associated with a dominant forest tree (Pinus ponderosa) in forests across ca. 550 km of geographic distance from northwestern to southeastern Arizona (USA). Both guilds of fungi showed distance decay, but drivers differed for each: ectomycorrhizal fungi are constrained primarily by dispersal limitation, whereas foliar endophytes are constrained by specific environmental conditions. Most ectomycorrhizal fungi were found in only a single forested area, as were many endophytic fungi. Such regional-scale perspectives are needed for baseline estimates of fungal diversity associated with forest trees at a landscape scale, with attention to the sensitivity of different guilds of fungal symbionts to decreasing areas of suitable habitat, increasing disturbance, and related impacts of climate change.
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Affiliation(s)
- Elizabeth A. Bowman
- grid.134563.60000 0001 2168 186XSchool of Plant Sciences, The University of Arizona, Tucson, AZ USA
| | - A. Elizabeth Arnold
- grid.134563.60000 0001 2168 186XSchool of Plant Sciences, The University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XDepartment of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ USA
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10
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Błaszczyk L, Salamon S, Mikołajczak K. Fungi Inhabiting the Wheat Endosphere. Pathogens 2021; 10:1288. [PMID: 34684238 PMCID: PMC8539314 DOI: 10.3390/pathogens10101288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 01/22/2023] Open
Abstract
Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.
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Affiliation(s)
- Lidia Błaszczyk
- Department of Plant Microbiomics, Institute of Plant Genetics, Polish Academy of Sciences, 34 Strzeszyńska Street, 60-479 Poznań, Poland; (S.S.); (K.M.)
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Ayesha MS, Suryanarayanan TS, Nataraja KN, Prasad SR, Shaanker RU. Seed Treatment With Systemic Fungicides: Time for Review. FRONTIERS IN PLANT SCIENCE 2021; 12:654512. [PMID: 34408757 PMCID: PMC8365024 DOI: 10.3389/fpls.2021.654512] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/06/2021] [Indexed: 05/27/2023]
Abstract
Pre-sowing seed treatment with systemic fungicides is a firmly entrenched practice for most agricultural crops worldwide. The treatment is intended to protect the crop against seed- and soil-borne diseases. In recent years, there is increasing evidence that fungicidal applications to manage diseases might inadvertently also affect non-target organisms, such as endophytes. Endophytes are ubiquitously present in plants and contribute to plant growth and development besides offering resistance to biotic and abiotic stresses. In seeds, endophytes may play a role in seed development, seed germination, seedling establishment and crop performance. In this paper, we review the recent literature on non-target effects of fungicidal applications on endophytic fungal community and discuss the possible consequences of indiscriminate seed treatment with systemic fungicide on seed endophytes. It is now well recognized that endophytes are ubiquitously present in all parts of the plant, including the seeds. They may be transmitted vertically from seed to seed as in many grasses and/or acquired horizontally from the soil and the environment. Though the origins and evolution of these organisms in plants are a matter of conjecture, numerous studies have shown that they symbiotically aid in plant growth and development, in nutrient acquisition as well in protecting the plants from abiotic and biotic stresses. Against this background, it is reasonable to assume that the use of systemic fungicides in seed treatment may not only affect the seed endophytes but also their attendant benefits to seedling growth and establishment. While there is evidence to indicate that fungicidal applications to manage plant diseases also affect foliar endophytes, there are only few studies that have documented the effect of seed treatment on seed-borne endophytes. Some of the convincing examples of the latter come from studies on the effect of fungicide application on rye grass seed endophyte AR37. More recently, experiments have shown that removal of seed endophytes by treatment with systemic fungicides leads to significant loss of seedling vigour and that such losses could be partially restored by enriching the seedlings with the lost endophytes. Put together, these studies reinforce the importance of seed endophytes to seedling growth and establishment and draw attention on how to trade the balance between the benefits of seed treatments and the direct and indirect costs incurred due to loss of endophytes. Among several approaches, use of reduced-risk fungicides and identifying fungicide-resistant endophytes are suggested to sustain the endophyte contribution to early seedling growth.
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Affiliation(s)
- Mulla S. Ayesha
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, India
| | | | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, India
| | | | - Ramanan Uma Shaanker
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore, India
- School of Ecology and Conservation, University of Agricultural Sciences, Bangalore, India
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12
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Oktalira FT, May TW, Dearnaley JDW, Linde CC. Seven new Serendipita species associated with Australian terrestrial orchids. Mycologia 2021; 113:968-987. [PMID: 34338610 DOI: 10.1080/00275514.2021.1919848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Serendipita is one of the main fungal genera that form mutualistic associations with species of orchids (Orchidaceae). Here, seven new Serendipita species associated with various Australian orchid genera are described. These Serendipita species were originally characterized by multilocus DNA sequence species delimitation analyses (three mtDNA and four nuclear genes) and confirmed as distinct with addition of further isolates and reanalysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S). Culture morphology and microscopic features are presented for each species, three of which are binucleate and four multinucleate. For the ITS region, the seven species have within-species sequence divergence between 1.07% and 4.31%, and all but one of the species pairs is separated by interspecific divergence of at least 4.35%. The newly described Serendipita species, S. australiana, S. communis, S. occidentalis, S. rarihospitum, S. secunda, S. talbotii, and S. warcupii, are shown to be separate species from S. vermifera on the basis of comparison against a sequence from the type. Isolates originally identified by Warcup as Sebacina "vermifera" from Caladenia orchids are revised and shown to belong to three of the species newly described here. Some non-Caladenia isolates identified by Warcup as S. "vermifera" are also shown to be non-conspecific with the type of S. vermifera. On the basis of ITS sequences, 346 isolates from 26 other studies, previously identified under provisional designations, are accommodated under the novel species. The species of Serendipta described here associate with the Australian orchid genera Caladenia, Cyanicula, Elythranthera, Ericksonella, Eriochilus, Glossodia, and Pheladenia. Most of the novel Serendipita species occur widely across Australia, often with widely distributed hosts, but one species, Serendipita rarihospitum, associates with narrowly distributed orchid species.
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Affiliation(s)
- Fitria T Oktalira
- Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - John D W Dearnaley
- Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland 4350, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
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Oita S, Carey J, Kline I, Ibáñez A, Yang N, Hom EFY, Carbone I, U'Ren JM, Arnold AE. Methodological Approaches Frame Insights into Endophyte Richness and Community Composition. MICROBIAL ECOLOGY 2021; 82:21-34. [PMID: 33410938 DOI: 10.1007/s00248-020-01654-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Isolating microbes is vital to study microbiomes, but insights into microbial diversity and ecology can be constrained by recalcitrant or unculturable strains. Culture-free methods (e.g., next-generation sequencing, NGS) have become popular in part because they detect greater richness than culturing alone. Both approaches are used widely to characterize microfungi within healthy leaves (foliar endophytes), but methodological differences among studies can constrain large-scale insights into endophyte ecology. We examined endophytes in a temperate plant community to quantify how certain methodological factors, such as the choice of cultivation media for culturing and storage period after leaf collection, affect inferences regarding endophyte communities; how such effects vary among plant taxa; and how complementary culturing and NGS can be when subsets of the same plant tissue are used for each. We found that endophyte richness and composition from culturing were consistent across five media types. Insights from culturing and NGS were largely robust to differences in storage period (1, 5, and 10 days). Although endophyte richness, composition, and taxonomic diversity identified via culturing vs. NGS differed markedly, both methods revealed host-structured communities. Studies differing only in cultivation media or storage period thus can be compared to estimate endophyte richness, composition, and turnover at scales larger than those of individual studies alone. Our data show that it is likely more important to sample more host species, rather than sampling fewer species more intensively, to quantify endophyte diversity in given locations, with the richest insights into endophyte ecology emerging when culturing and NGS are paired.
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Affiliation(s)
- Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jamison Carey
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Ian Kline
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Alicia Ibáñez
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Nathaniel Yang
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Erik F Y Hom
- Department of Biology, Center for Biodiversity & Conservation Research, University of Mississippi, University, MS, 38677, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jana M U'Ren
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.
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14
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Silva PS, Royo VA, Valerio HM, Fernandes EG, Queiroz MV, Fagundes M. Filtrates from cultures of endophytic fungi isolated from leaves of Copaifera oblongifolia (Fabaceae) affect germination and seedling development differently. BRAZ J BIOL 2021; 83:e242070. [PMID: 34161452 DOI: 10.1590/1519-6984.242070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/28/2021] [Indexed: 11/22/2022] Open
Abstract
Interactions between endophytic fungi (EFs) and their host plants range from positive to neutral to negative. The results of such interactions can vary depending on the organ of the infected host plant. EFs isolated from the leaves of some species of plants have potential for use as agents to inhibit seed germination and control invasive plants. The objectives of this study were to identify EFs present in the leaves of Copaifera oblongifolia and to evaluate the role of these fungi in seed germination and seedling development. A total of 11 species of EFs were isolated, which were identified using the internal transcribed spacers (ITS) sequence of the nuclear ribosomal DNA. The isolated species of EFs are generalists and probably are transmitted horizontally. Laboratory tests revealed that filtrates of these fungal isolates differently affect seed germination and seedling development of C. oblongifolia. The species Curvularia intermedia, Neofusicoccum parvum, Pseudofusicoccum stromaticum and Phomopsis sp. negatively affected seed germination, with N. parvum standing out for its negative effects, inhibiting seedling germination and survival in 89 and 222%, respectively. In addition, Cochliobolus intermedius negatively affected seedling development. Thus, the combined use of N. parvum and C. intermedius, or products from the metabolism of these microorganisms, in the control of invasive plants deserves attention from future studies.
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Affiliation(s)
- P S Silva
- Universidade Estadual de Montes Claros - Unimontes, Departamento de Biologia Geral, Programa de Pós-graduação em Biodiversidade e Uso dos Recursos Naturais, Montes Claros, MG, Brasil
| | - V A Royo
- Universidade Estadual de Montes Claros - Unimontes, Departamento de Biologia Geral, Programa de Pós-graduação em Biodiversidade e Uso dos Recursos Naturais, Montes Claros, MG, Brasil
| | - H M Valerio
- Universidade Estadual de Montes Claros - Unimontes, Departamento de Biologia Geral, Programa de Pós-graduação em Biodiversidade e Uso dos Recursos Naturais, Montes Claros, MG, Brasil
| | - E G Fernandes
- Universidade Estadual de Montes Claros - Unimontes, Departamento de Biologia Geral, Programa de Pós-graduação em Biodiversidade e Uso dos Recursos Naturais, Montes Claros, MG, Brasil
| | - M V Queiroz
- Universidade Federal de Viçosa - UFV, Instituto de Biotecnologia Aplicada à Agropecuária - BIOAGRO, Departamento de Microbiologia, Laboratório de Genética Molecular de Fungos, Viçosa, MG, Brasil
| | - M Fagundes
- Universidade Estadual de Montes Claros - Unimontes, Departamento de Biologia Geral, Programa de Pós-graduação em Biodiversidade e Uso dos Recursos Naturais, Montes Claros, MG, Brasil
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15
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Mao Z, Zhang W, Wu C, Feng H, Peng Y, Shahid H, Cui Z, Ding P, Shan T. Diversity and antibacterial activity of fungal endophytes from Eucalyptus exserta. BMC Microbiol 2021; 21:155. [PMID: 34044780 PMCID: PMC8157698 DOI: 10.1186/s12866-021-02229-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/12/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Eucalyptus bacterial wilt caused by Ralstonia solanacearum is an important eucalyptus disease. Endophytic fungi, an important source of natural active substances, provide a new breakthrough for the control of plant diseases. RESULTS In the present study, 80 endophytic fungal isolates were obtained from the healthy branches and fruits of Eucalyptus exserta. Fifteen distinct isolates (MK120854-MK120868) were selected for further taxonomic identification through morphological trait assessments and internal transcribed spacer (ITS) region-rRNA gene sequence analysis. Thirteen genera, namely, Phyllosticta, Penicillium, Eutypella, Purpureocillium, Talaromyces, Lophiostoma, Cladosporium, Pestalotiopsis, Chaetomium, Fusarium, Gongronella, Scedosporium and Pseudallescheria, were identified on the basis of their morphological characteristics. Members of the genus Phyllosticta were the primary isolates, with a colonization frequency (CF) of 27.5 %. Most of the fungal isolates displayed antibacterial activity. The crude extracts obtained from Lophiostoma sp. Eef-7, Pestalotiopsis sp. Eef-9 and Chaetomium sp. Eef-10 exhibited strong inhibition on the test bacteria, and Lophiostoma sp. Eef-7 was further cultured on a large scale. Three known compounds, scorpinone (1), 5-deoxybostrycoidin (2) and 4-methyl-5,6-dihydro-2 H-pyran-2-one (3), were isolated from the endophytic fungus Lophiostoma sp. Eef-7 associated with E. exserta. The structures of these compounds were elucidated by analysis of 1D and 2D NMR and HR-ESI-MS spectra and a comparison of their spectral data with published values. Compounds 1 and 2 showed weak antimicrobial activity against Ralstonia solanacearum. CONCLUSIONS Endophytic fungi from Eucalyptus exserta may represent alternative sources of antimicrobial agents. Lophiostoma sp. Eef-7 can produce 2-azaanthraquinone derivatives and shows weak antibacterial activity against Ralstonia solanacearum.
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Affiliation(s)
- Ziling Mao
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Weihao Zhang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Chunyin Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Hao Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Yuanhang Peng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Hamza Shahid
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China
| | - Zining Cui
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, 510642, Guangzhou, China
| | - Ping Ding
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No. 232, Waihuandong Road, Panyu District, Guangdong, 510006, Guangzhou, China.
| | - Tijiang Shan
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, 510642, No. 483, Wushan Road, Tianhe District, Guangdong, 510642, Guangzhou, China.
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16
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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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17
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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18
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Oita S, Ibáñez A, Lutzoni F, Miadlikowska J, Geml J, Lewis LA, Hom EFY, Carbone I, U'Ren JM, Arnold AE. Climate and seasonality drive the richness and composition of tropical fungal endophytes at a landscape scale. Commun Biol 2021; 4:313. [PMID: 33750915 PMCID: PMC7943826 DOI: 10.1038/s42003-021-01826-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding how species-rich communities persist is a foundational question in ecology. In tropical forests, tree diversity is structured by edaphic factors, climate, and biotic interactions, with seasonality playing an essential role at landscape scales: wetter and less seasonal forests typically harbor higher tree diversity than more seasonal forests. We posited that the abiotic factors shaping tree diversity extend to hyperdiverse symbionts in leaves-fungal endophytes-that influence plant health, function, and resilience to stress. Through surveys in forests across Panama that considered climate, seasonality, and covarying biotic factors, we demonstrate that endophyte richness varies negatively with temperature seasonality. Endophyte community structure and taxonomic composition reflect both temperature seasonality and climate (mean annual temperature and precipitation). Overall our findings highlight the vital role of climate-related factors in shaping the hyperdiversity of these important and little-known symbionts of the trees that, in turn, form the foundations of tropical forest biodiversity.
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Affiliation(s)
- Shuzo Oita
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | | | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, Eger, Hungary
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Erik F Y Hom
- Department of Biology, Center for Biodiversity and Conservation Research, University of Mississippi, University, MS, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jana M U'Ren
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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19
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Saadani M, Hönig L, Bien S, Koehler M, Rutten G, Wubet T, Braun U, Bruelheide H. Local Tree Diversity Suppresses Foliar Fungal Infestation and Decreases Morphological But Not Molecular Richness in a Young Subtropical Forest. J Fungi (Basel) 2021; 7:173. [PMID: 33673628 PMCID: PMC7997179 DOI: 10.3390/jof7030173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022] Open
Abstract
Leaf fungal pathogens alter their host species' performance and, thus, changes in fungal species composition can translate into effects at the tree community scale. Conversely, the functional diversity of tree species in a host tree's local neighbourhood can affect the host's foliar fungal infestation. Therefore, understanding the factors that affect fungal infestations is important to advance our understanding of biodiversity-ecosystem functioning (BEF) relationships. Here we make use of the largest BEF tree experiment worldwide, the BEF-China experiment, where we selected tree host species with different neighbour species. Identifying fungal taxa by microscopy and by high-throughput DNA sequencing techniques based on the internal transcribed spacer (ITS) rDNA region, we analysed the fungal richness and infestation rates of our target trees as a function of local species richness. Based on the visual microscopic assessment, we found that a higher tree diversity reduced fungal richness and host-specific fungal infestation in the host's local neighbourhood, while molecular fungal richness was unaffected. This diversity effect was mainly explained by the decrease in host proportion. Thus, the dilution of host species in the local neighbourhood was the primary mechanism in reducing the fungal disease severity. Overall, our study suggests that diverse forests will suffer less from foliar fungal diseases compared to those with lower diversity.
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Affiliation(s)
- Mariem Saadani
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Lydia Hönig
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Steffen Bien
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Michael Koehler
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Gemma Rutten
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
- Department of Community Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120 Halle, Germany
| | - Uwe Braun
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany; (L.H.); (S.B.); (M.K.); (G.R.); (U.B.); (H.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103 Leipzig, Germany;
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20
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Bioactive Attributes of Xylaria Species from the Scrub Jungles of Southwest India. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Dalling JW, Davis AS, Arnold AE, Sarmiento C, Zalamea PC. Extending Plant Defense Theory to Seeds. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-012120-115156] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plant defense theory explores how plants invest in defenses against natural enemies but has focused primarily on the traits expressed by juvenile and mature plants. Here we describe the diverse ways in which seeds are chemically and physically defended. We suggest that through associations with other traits, seeds are likely to exhibit defense syndromes that reflect constraints or trade-offs imposed by selection to attract dispersers, enable effective dispersal, ensure appropriate timing of seed germination, and enhance seedling performance. We draw attention to seed and reproductive traits that are analogous to defense traits in mature plants and describe how the effectiveness of defenses is likely to differ at pre- and postdispersal stages. We also highlight recent insights into the mutualistic and antagonistic interactions between seeds and microbial communities, including fungi and endohyphal bacteria, that can influence seed survival in the soil and subsequent seedling vigor.
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Affiliation(s)
- James W. Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, República de Panamá
| | - Adam S. Davis
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - A. Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Carolina Sarmiento
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, República de Panamá
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA;,
| | - Paul-Camilo Zalamea
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Panamá, República de Panamá
- Department of Integrative Biology, University of South Florida, Tampa, Florida 33620, USA;,
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22
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Relationships between Foliar Fungal Endophyte Communities and Ecophysiological Traits of CAM and C3 Epiphytic Bromeliads in a Neotropical Rainforest. DIVERSITY 2020. [DOI: 10.3390/d12100378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vascular epiphytes contribute up to 35% of the plant diversity and foliar biomass of flowering plants. The family Bromeliaceae is a monophyletic group of plants native to the Neotropics. Epiphytic bromeliads form associations with distinct groups of organisms but their relationship with foliar fungal endophytes remain underexplored. In this study we examined the relationship of foliar fungal endophytes to host photosynthetic pathways and associated ecophysiological traits. We sampled the fungal endophyte communities of 67 host individuals in six epiphytic bromeliad species differing in C3 and crassulacean acid metabolism (CAM) photosynthetic pathways. We tested whether endophyte assemblages were associated with ecophysiological leaf traits related to host photosynthetic pathways. Our results indicate that (1) C3 and CAM bromeliads host dissimilar endophyte assemblages, (2) endophyte communities in C3 bromeliads are characterized by variable relative abundances of fungal orders; conversely, CAM associated endophyte communities were characterized by consistent relative abundances of fungal orders, and (3) endophyte communities in bromeliads are distributed along a continuum of leaf toughness and leaf water content. Taken together, our study suggests that host physiology and associated ecophysiological traits of epiphytic bromeliads may represent biotic filters for communities of fungal endophytes in the tropics.
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23
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Toghueo RMK, Sahal D, Boyom FF. Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers. PHYTOCHEMISTRY 2020; 174:112338. [PMID: 32179305 DOI: 10.1016/j.phytochem.2020.112338] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
Today when the quest of new lead molecules to supply the development pipeline is driving the course of drug discovery, endophytic fungi with their outstanding biosynthetic potential seem to be highly promising avenues for natural product scientists. However, challenges such as the production of inadequate quantities of compounds, the attenuation or loss of ability of endophytes to produce the compound of interest when grown in culture and the inability of fungal endophytes to express their full biosynthetic potential in laboratory conditions have been the major constraints. These have led to the application of small chemical elicitors that induce epigenetic changes in fungi to activate their silent gene clusters optimizing the amount of metabolites of interest or inducing the synthesis of hitherto undescribed compounds. In this respect small molecular weight compounds which are known to function as inhibitors of histone deacetylase (HDAC), DNA methyltransferase (DNMT) and proteasome have proven their efficacy in enhancing or inducing the production of specialized metabolites by fungi. Moreover, organic solvents, metals and plants extracts are also acknowledged for their ability to cause shifts in fungal metabolism. We highlight the successful studies from the past two decades reporting the ability of structurally diverse small molecular weight compounds to elicit the production of previously undescribed metabolites from endophytic fungi grown in culture. This mini review argues in favor of chemical elicitation as an effective strategy to optimize the production of fungal metabolites and invigorate the pipeline of drug discovery with new chemical entities.
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Affiliation(s)
- Rufin Marie Kouipou Toghueo
- Antimicrobial and Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon.
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Fabrice Fekam Boyom
- Antimicrobial and Biocontrol Agents Unit (AmBcAU), Laboratory for Phytobiochemistry and Medicinal Plants Studies, Department of Biochemistry, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon.
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Gupta S, Chaturvedi P, Kulkarni MG, Van Staden J. A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. Biotechnol Adv 2020; 39:107462. [DOI: 10.1016/j.biotechadv.2019.107462] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 02/08/2023]
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Li YM, Shaffer JP, Hall B, Ko H. Soil-borne fungi influence seed germination and mortality, with implications for coexistence of desert winter annual plants. PLoS One 2019; 14:e0224417. [PMID: 31671129 PMCID: PMC6822719 DOI: 10.1371/journal.pone.0224417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/14/2019] [Indexed: 11/25/2022] Open
Abstract
Soil-borne fungi influence coexistence of plant species in mesic environments, but much less is known about their effects on demographic processes relevant to coexistence in arid and semi-arid systems. We isolated 43 fungal strains that naturally colonize seeds of an invasive winter annual (Brassica tournefortii) in the Sonoran Desert, and evaluated the impact of 18 of them on seed germination and mortality of B. tournefortii and a co-occurring native annual (Plantago ovata) under simulated summer and winter temperatures. Fungi isolated from B. tournefortii seeds impacted germination and mortality of seeds of both plant species in vitro. Seed responses reflected host-specific effects by fungi, the degree of which differed significantly between the strains, and depended on the temperature. In the winter temperature, ten fungal strains increased or reduced seed germination, but substantial seed mortality due to fungi was not observed. Two strains increased germination of P. ovata more strongly than B. tournefortii. In the summer temperature, fungi induced both substantial seed germination and mortality, with ten strains demonstrating host-specificity. Under natural conditions, host-specific effects of fungi on seed germination may further differentiate plant species niche in germination response, with a potential of promoting coexistence. Both host-specific and non-host-specific effects of fungi on seed loss may induce polarizing effects on plant coexistence depending on the ecological context. The coexistence theory provides a clear framework to interpret these polarizing effects. Moreover, fungi pathogenic to both plant species could induce host-specific germination, which challenges the theoretical assumption of density-independent germination response. These implications from an in vitro study underscore the need to weave theoretical modeling, reductive empirical experiments, and natural observations to illuminate effects of soil-borne fungi on coexistence of annual plant species in variable desert environments.
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Affiliation(s)
- Yue M. Li
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States of America
- Arizona-Sonora Desert Museum, Tucson, Arizona, United States of America
| | - Justin P. Shaffer
- School of Plant Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Brenna Hall
- College of Public Health, University of Arizona, Tucson, Arizona, United States of America
| | - Hongseok Ko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States of America
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Leroy C, Maes AQ, Louisanna E, Séjalon-Delmas N. How significant are endophytic fungi in bromeliad seeds and seedlings? Effects on germination, survival and performance of two epiphytic plant species. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Gordillo A, Decock C. Multigene phylogenetic and morphological evidence for seven new species of Aquanectria and Gliocladiopsis (Ascomycota, Hypocreales) from tropical areas. Mycologia 2019; 111:299-318. [PMID: 30924725 DOI: 10.1080/00275514.2018.1548863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aquanectria and Gliocladiopsis are two closely related genera of Hypocreales. They are also morphologically similar, forming hyaline, penicillate conidiophores and hyaline, straight to sinuous, 0-1-septate phialoconidia. During a revision of gliocladiopsis-like isolates originating from rain forest areas of South America (Ecuador, French Guiana) and Southeast Asia (Singapore), multilocus phylogenetic inferences, based on DNA sequences encoding partial β-tubulin (TUB2), translation elongation factor 1-α (TEF1- α), histone H3 (HIS3) genes and the nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), revealed the occurrence of seven new phylogenetic species. These phylogenetic species also revealed unique combinations of phenotypes, allowing morphological distinction from their closest phylogenetic relatives. Four new species of Aquanectria and three new species of Gliocladiopsis are described and illustrated. Three of the four Aquanectria species deviate from the other species in the genus by having shorter conidia, which are in the size range observed in Gliocladiopsis species. They are placed in Aquanectria based on the phylogenetic analysis, but this also makes the morphological distinction between these two genera obsolete.
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Affiliation(s)
- Ana Gordillo
- a Laboratorio de Micología, Pontificia, Universidad Católica del Ecuador , Quito , Ecuador.,b Earth and Life Institute, Mycothèque de l'Université catholique de Louvain (MUCL) , Croix du Sud 2 bte L7/05.06, 1348 Louvain-la-Neuve , Belgium
| | - Cony Decock
- b Earth and Life Institute, Mycothèque de l'Université catholique de Louvain (MUCL) , Croix du Sud 2 bte L7/05.06, 1348 Louvain-la-Neuve , Belgium
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Shaffer JP, Zalamea PC, Sarmiento C, Gallery RE, Dalling JW, Davis AS, Baltrus DA, Arnold AE. Context-dependent and variable effects of endohyphal bacteria on interactions between fungi and seeds. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Daru BH, Bowman EA, Pfister DH, Arnold AE. A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170395. [PMID: 30455213 PMCID: PMC6282087 DOI: 10.1098/rstb.2017.0395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2018] [Indexed: 12/22/2022] Open
Abstract
Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome (Andromeda polifolia and Ledum palustre subsp. groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years. We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
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Affiliation(s)
- Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA
| | | | - Donald H Pfister
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Whitaker BK, Reynolds HL, Clay K. Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass). Ecology 2018; 99:2703-2711. [PMID: 30367461 DOI: 10.1002/ecy.2543] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/06/2018] [Accepted: 10/02/2018] [Indexed: 11/06/2022]
Abstract
Experimental tests of community assembly mechanisms for host-associated microbiomes in nature are lacking. Asymptomatic foliar fungal endophytes are a major component of the plant microbiome and are increasingly recognized for their impacts on plant performance, including pathogen defense, hormonal manipulation, and drought tolerance. However, it remains unclear whether fungal endophytes preferentially colonize certain host ecotypes or genotypes, reflecting some degree of biotic adaptation in the symbioses, or whether colonization is simply a function of spore type and abundance within the local environment. Whether host ecotype, local environment, or some combination of both controls the pattern of microbiome formation across hosts represents a new dimension to the age-old debate of nature versus nurture. Here, we used a reciprocal transplant design to explore the extent of host specificity and biotic adaptation in the plant microbiome, as evidenced by differential colonization of host genetic types by endophytes. Specifically, replicate plants from three locally-adapted ecotypes of the native grass Panicum virgatum (switchgrass) were transplanted at three geographically distinct field sites (one home and two away) in the Midwestern US. At the end of the growing season, plant leaves were harvested and the fungal microbiome characterized using culture-dependent sequencing techniques. Our results demonstrated that fungal endophyte community structure was determined by local environment (i.e., site), but not by host ecotype. Fungal richness and diversity also strongly differed by site, with lower fungal diversity at a riparian field site, whereas host ecotype had no effect. By contrast, there were significant differences in plant phenotypes across all ecotypes and sites, indicating ecotypic differentiation of host phenotype. Overall, our results indicate that environmental factors are the primary drivers of community structure in the switchgrass fungal microbiome.
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Affiliation(s)
- Briana K Whitaker
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA.,Department of Plant & Microbial Biology, North Carolina State University, Box 7612, Raleigh, North Carolina, 27695-7612, USA
| | - Heather L Reynolds
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA
| | - Keith Clay
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA.,Department of Ecology & Evolutionary Biology, Tulane University, 6823 St,. Charles Ave., New Orleans, Louisiana, 70118, USA
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Man B, Wang H, Yun Y, Xiang X, Wang R, Duan Y, Cheng X. Diversity of Fungal Communities in Heshang Cave of Central China Revealed by Mycobiome-Sequencing. Front Microbiol 2018; 9:1400. [PMID: 30061866 PMCID: PMC6054936 DOI: 10.3389/fmicb.2018.01400] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 06/07/2018] [Indexed: 11/13/2022] Open
Abstract
Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumina HiSeq sequencing of fungal rRNA-ITS1 gene across different habitats. In total 793,502 ITS1 reads and 2,179 OTUs from 778 Mb reads after stringent quality control (Q30) and 453 genera, 72 orders and 19 classes within 6 phyla were detected. Ascomycota (42% OTUs) dominated across the five habitats. Shannon-Wiener index varied from 1.25 to 7.62 and community richness was highest in drip waters, followed by weathered rocks, bat guanos, sediments, and air samples. Mycobiomes displayed specificity to five habitats and more distinct OTUs were found in weathered rocks (12%) and drip waters (9%). In contrast, only 6.60% core OTUs were shared by five habitats. Notably, weathered rocks possessed more indicator groups and were revealed for the first time to be dominated by Sordariomycetes (43%). The community richness of air mycobiomes increased from cave entrance to the innermost part and dominated by the indicator groups of Penicillium mallochii (>30%) and P. herquei (>9%). Our work represents the largest attempt to date to a systematical investigation of oligotrophic solution-cave-associated mycobiomes in China. Our discovery of high diversity of mycobiomes in Heshang Cave also suggests that eukaryotic microorganisms may play a crucial role in subsurface environments.
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Affiliation(s)
- Baiying Man
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,College of Life Science, Shangrao Normal University, Shangrao, China
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.,Laboratory of Basin Hydrology and Wetland Eco-restoration, China University of Geosciences, Wuhan, China
| | - Yuan Yun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xing Xiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Yong Duan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Xiaoyu Cheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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Scott M, Rani M, Samsatly J, Charron JB, Jabaji S. Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds. Can J Microbiol 2018; 64:664-680. [PMID: 29911410 DOI: 10.1139/cjm-2018-0108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.
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Affiliation(s)
- Maryanne Scott
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Mamta Rani
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jamil Samsatly
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jean-Benoit Charron
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Suha Jabaji
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
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Chen KH, Liao HL, Arnold AE, Bonito G, Lutzoni F. RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi. THE NEW PHYTOLOGIST 2018; 218:1597-1611. [PMID: 29604236 DOI: 10.1111/nph.15092] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/07/2018] [Indexed: 05/15/2023]
Abstract
Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.
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Affiliation(s)
- Ko-Hsuan Chen
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Hui-Ling Liao
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Soil and Water Sciences Department, North Florida Research and Education Center, University of Florida, Quincy, FL, 32351, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
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Husbands DR, Urbina H, Lewis SM, Aime MC. Xylaria karyophthora: a new seed-inhabiting fungus of Greenheart from Guyana. Mycologia 2018; 110:434-447. [PMID: 29792784 DOI: 10.1080/00275514.2018.1457349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Dillon R. Husbands
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Hector Urbina
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Susy M. Lewis
- Department of Forestry, University of Guyana, Turkeyen Campus, Greater Georgetown, Guyana
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
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Bowman EA, Arnold AE. Distributions of ectomycorrhizal and foliar endophytic fungal communities associated with Pinus ponderosa along a spatially constrained elevation gradient. AMERICAN JOURNAL OF BOTANY 2018; 105:687-699. [PMID: 29756204 DOI: 10.1002/ajb2.1072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/22/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Understanding distributions of plant-symbiotic fungi is important for projecting responses to environmental change. Many coniferous trees host ectomycorrhizal fungi (EM) in association with roots and foliar endophytic fungi (FE) in leaves. We examined how EM and FE associated with Pinus ponderosa each vary in abundance, diversity, and community structure over a spatially constrained elevation gradient that traverses four plant communities, 4°C in mean annual temperature, and 15 cm in mean annual precipitation. METHODS We sampled 63 individuals of Pinus ponderosa in 10 sites along a 635 m elevation gradient that encompassed a geographic distance of 9.8 km. We used standard methods to characterize each fungal group (amplified and sequenced EM from root tips; isolated and sequenced FE from leaves). KEY RESULTS Abundance and diversity of EM were similar across sites, but community composition and distributions of the most common EM differed with elevation (i.e., with climate, soil chemistry, and plant communities). Abundance and composition of FE did not differ with elevation, but diversity peaked in mid-to-high elevations. CONCLUSIONS Our results suggest relatively tight linkages between EM and climate, soil chemistry, and plant communities. That FE appear less linked with these factors may speak to limitations of a culture-based approach, but more likely reflects the small spatial scale encompassed by our study. Future work should consider comparable methods for characterizing these functional groups, and additional transects to understand relationships of EM and FE to environmental factors that are likely to shift as a function of climate change.
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Affiliation(s)
- Elizabeth A Bowman
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona, 85721, USA
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36
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Dastogeer KMG, Li H, Sivasithamparam K, Jones MGK, Wylie SJ. Host Specificity of Endophytic Mycobiota of Wild Nicotiana Plants from Arid Regions of Northern Australia. MICROBIAL ECOLOGY 2018; 75:74-87. [PMID: 28702707 DOI: 10.1007/s00248-017-1020-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
In arid regions of northern Australia, plants survive under water deficit, high temperatures, intense solar radiation and nutrient-impoverished soils. They employ various morpho-physiological and biochemical adaptations including interaction with microbial symbionts. We evaluated identity, host and tissue association with geographical distribution of fungal endophytes isolated from above- and below-ground tissues of plants of three indigenous Australian Nicotiana species. Isolation frequency and α-diversity were significantly higher for root endophyte assemblages than those of stem and leaf tissues. We recorded no differences in endophyte species richness or diversity as a function of sampling location, but did detect differences among different host genotypes and plant tissues. There was a significant pattern of community similarity associated with host genotypes but no consistent pattern of fungal community structuring associated with sampling location and tissue type, regardless of the community similarity measurements used.
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Affiliation(s)
- Khondoker M G Dastogeer
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 6150, Australia
| | - Hua Li
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 6150, Australia
| | - Krishnapillai Sivasithamparam
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 6150, Australia
| | - Michael G K Jones
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 6150, Australia
| | - Stephen J Wylie
- Plant Biotechnology Group - Plant Virology, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, 6150, Australia.
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37
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Seed-associated fungi in the alpine tundra: Both mutualists and pathogens could impact plant recruitment. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Dornburg A, Townsend JP, Wang Z. Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. ADVANCES IN GENETICS 2017; 100:1-47. [PMID: 29153398 DOI: 10.1016/bs.adgen.2017.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine. However, the rise of big data has also presented phylogenomicists with a new set of challenges to experimental design, quantitative analyses, and computation. The sequencing of a number of very first genomes presented significant challenges to phylogenetic inference, leading fungal phylogenomicists to begin addressing pitfalls and postulating solutions to the issues that arise from genome-scale analyses relevant to any lineage across the Tree of Life. Here we highlight insights from fungal phylogenomics for topics including systematics and species delimitation, ecological and phenotypic diversification, and biogeography while providing an overview of progress made on the reconstruction of the fungal Tree of Life. Finally, we provide a review of considerations to phylogenomic experimental design for robust tree inference. We hope that this special issue of Advances in Genetics not only excites the continued progress of fungal evolutionary biology but also motivates the interdisciplinary development of new theory and methods designed to maximize the power of genomic scale data in phylogenetic analyses.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, United States
| | | | - Zheng Wang
- Yale University, New Haven, CT, United States.
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39
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Soilborne fungi have host affinity and host-specific effects on seed germination and survival in a lowland tropical forest. Proc Natl Acad Sci U S A 2017; 114:11458-11463. [PMID: 28973927 DOI: 10.1073/pnas.1706324114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Janzen-Connell (JC) hypothesis provides a conceptual framework for explaining the maintenance of tree diversity in tropical forests. Its central tenet-that recruits experience high mortality near conspecifics and at high densities-assumes a degree of host specialization in interactions between plants and natural enemies. Studies confirming JC effects have focused primarily on spatial distributions of seedlings and saplings, leaving major knowledge gaps regarding the fate of seeds in soil and the specificity of the soilborne fungi that are their most important antagonists. Here we use a common garden experiment in a lowland tropical forest in Panama to show that communities of seed-infecting fungi are structured predominantly by plant species, with only minor influences of factors such as local soil type, forest characteristics, or time in soil (1-12 months). Inoculation experiments confirmed that fungi affected seed viability and germination in a host-specific manner and that effects on seed viability preceded seedling emergence. Seeds are critical components of reproduction for tropical trees, and the factors influencing their persistence, survival, and germination shape the populations of seedlings and saplings on which current perspectives regarding forest dynamics are based. Together these findings bring seed dynamics to light in the context of the JC hypothesis, implicating them directly in the processes that have emerged as critical for diversity maintenance in species-rich tropical forests.
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Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Kauff F, U'Ren JM, May G, Lutzoni F. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life. Bioinformatics 2017; 33:1160-1168. [PMID: 28003260 DOI: 10.1093/bioinformatics/btw808] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. Results In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. Availability and Implementation T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. Contact icarbon@ncsu.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | - James B White
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695 USA
| | | | - A Elizabeth Arnold
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA.,Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Mark A Miller
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Frank Kauff
- Department of Medicine, University of Giessen, Giessen, Germany
| | - Jana M U'Ren
- School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
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Phylogenetic relationships and spatial distributions of putative fungal pathogens of seedlings across a rainfall gradient in Panama. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2016.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Shaffer JP, U'Ren JM, Gallery RE, Baltrus DA, Arnold AE. An Endohyphal Bacterium ( Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum ( F. solani Species Complex, Nectriaceae). Front Microbiol 2017; 8:350. [PMID: 28382021 PMCID: PMC5361657 DOI: 10.3389/fmicb.2017.00350] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/20/2017] [Indexed: 01/12/2023] Open
Abstract
Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions.
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Affiliation(s)
| | - Jana M U'Ren
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Agricultural and Biosystems Engineering, University of ArizonaTucson, AZ, USA
| | - Rachel E Gallery
- School of Natural Resources and the Environment, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona Tucson, AZ, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, University of ArizonaTucson, AZ, USA; Department of Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, USA
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Crouch JA, Clarke BB, White JF, Hillman BI. Systematic analysis of the falcate-spored graminicolous Colletotrichum and a description of six new species from warm-season grasses. Mycologia 2017; 101:717-32. [DOI: 10.3852/08-230] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Bradley I. Hillman
- Rutgers University, Department of Plant Biology and Pathology, 59 Dudley Road, New Brunswick, New Jersey 08901
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Higgins KL, Coley PD, Kursar TA, Arnold AE. Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses. Mycologia 2017; 103:247-60. [DOI: 10.3852/09-158] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Thomas A. Kursar
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - A. Elizabeth Arnold
- Division of Plant Pathology and Microbiology, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
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Rojas EI, Rehner SA, Samuels GJ, Van Bael SA, Herre EA, Cannon P, Chen R, Pang J, Wang R, Zhang Y, Peng YQ, Sha T. Colletotrichum gloeosporioidess.l. associated withTheobroma cacaoand other plants in Panamá: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia 2017; 102:1318-38. [DOI: 10.3852/09-244] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Gary J. Samuels
- USDA-ARS, Systematic Mycology and Microbiology Laboratory, Beltsville, Maryland 20705
| | | | - Edward A. Herre
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Republic of Panamá
| | - Paul Cannon
- CABI, Bakeham Lane, Egham, TW20 9TY, UK and Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | | | | | | | - Yaping Zhang
- State Key Laboratories, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, People’s Republic of China
| | - Yan-Qiong Peng
- Key Laboratory of Tropical Forest Ecology, Xinshiabanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People’s Republic of China
| | - Tao Sha
- Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming 650091, People’s Republic of China
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Karst J, Piculell B, Brigham C, Booth M, Hoeksema JD. Fungal communities in soils along a vegetative ecotone. Mycologia 2017; 105:61-70. [DOI: 10.3852/12-042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Justine Karst
- University of Mississippi, Department of Biology, PC) Box 1848, Oxford, Mississippi 38677
| | - Bridget Piculell
- University of Mississippi, Department of Biology, PC) Box 1848, Oxford, Mississippi 38677
| | - Christy Brigham
- Santa Monica Mountains National Recreation Area, 401 West Hillcrest Drive, Thousand Oaks, California 91360
| | - Michael Booth
- Institute of Arctic Biology, University of Alaska. PO Box 757000. Fairbanks. Alaska 99775
| | - Jason D Hoeksema
- University of Mississippi, Department of Biology, PC) Box 1848, Oxford, Mississippi 38677
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U'Ren JM, Arnold AE. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. PeerJ 2016; 4:e2768. [PMID: 27994976 PMCID: PMC5157190 DOI: 10.7717/peerj.2768] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 11/07/2016] [Indexed: 12/17/2022] Open
Abstract
Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Discussion Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.
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Affiliation(s)
- Jana M U'Ren
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States of America; Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, United States of America
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States of America; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States of America
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Community structure of fern-affiliated endophytes in three neotropical forests. JOURNAL OF TROPICAL ECOLOGY 2016. [DOI: 10.1017/s0266467416000535] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract:From the saprotrophs that decay plant material to the pathogens and mutualists that shape plant demography at local and regional scales, fungi are major drivers of tropical forest dynamics. Although endophytic fungi are abundant and diverse in many biomes, they reach their greatest diversity in tropical forests, where they can influence plant physiology, performance and survival. The number of quantitative studies regarding endophytes has increased dramatically in the past two decades, but general rules have not yet emerged regarding the biogeography, host affiliations, local or regional distributions, or phylogenetic diversity of endophytes in most tropical settings. Here, endophytic fungal communities associated with 18 species of eupolypod fern were compared among forest reserves in Panama, Costa Rica and Mexico. Molecular sequence data for >2000 isolates were used to determine the relationships of host taxonomy, forest (site), and environmental dissimilarity to endophyte community composition. Communities in related ferns differed significantly among forests, reflecting the interplay of geographic distance and environmental dissimilarity. Although the same phyla and classes of fungi were prevalent at each site, they differed in relative abundance. All sites were dominated by the same order (Xylariales), but sites differed in the phylogenetic clustering vs. evenness of their endophyte communities. By addressing the relationship of endophyte communities to host taxonomy, geographic distance and environmental factors, this study complements previous work on angiosperms and contributes to a growing perspective on the factors shaping communities of ecologically important fungi in tropical forests.
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Shaffer JP, Sarmiento C, Zalamea PC, Gallery RE, Davis AS, Baltrus DA, Arnold AE. Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Izuno A, Tanabe AS, Toju H, Yamasaki M, Indrioko S, Isagi Y. Structure of phyllosphere fungal communities in a tropical dipterocarp plantation: A massively parallel next-generation sequencing analysis. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2015.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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